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2017 | OriginalPaper | Buchkapitel

37. Applications of Computational Methods to Simulations of Proteins Dynamics

verfasst von : Wieslaw Nowak

Erschienen in: Handbook of Computational Chemistry

Verlag: Springer International Publishing

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Abstract

The present advanced state of the computer hardware offers superb opportunities for further explorations of protein structure and dynamics. Sound and well-established theoretical models are successfully used for searching new biochemical phenomena, correlations, and protein properties. In this chapter, the fast-growing field of computer simulations of protein dynamics is panoramically presented. The principles of currently used computational methods are briefly outlined, and representative examples of their recent advanced applications are given. In particular protein folding studies, intrinsically disordered proteins, protein-drug interactions, ligand transport phenomena, ion channel activity, molecular machine mechanics, origins of molecular diseases, and simulations of single-molecule AFM experiments are addressed. Special attention is devoted to emerging methods of enhanced molecular dynamics.

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Literatur
Zurück zum Zitat Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., et al. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25.CrossRef Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., et al. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25.CrossRef
Zurück zum Zitat Abrams, C., & Bussi, G. (2013). Enhanced sampling in molecular dynamics using metadynamics, replica-exchange, and temperature-acceleration. Entropy, 16(1), 163.CrossRef Abrams, C., & Bussi, G. (2013). Enhanced sampling in molecular dynamics using metadynamics, replica-exchange, and temperature-acceleration. Entropy, 16(1), 163.CrossRef
Zurück zum Zitat Achary, M. S., & Nagarajaram, H. A. (2009). Effects of disease causing mutations on the essential motions in proteins. Journal of Biomolecular Structure and Dynamics, 26(5), 609–624.CrossRef Achary, M. S., & Nagarajaram, H. A. (2009). Effects of disease causing mutations on the essential motions in proteins. Journal of Biomolecular Structure and Dynamics, 26(5), 609–624.CrossRef
Zurück zum Zitat Adcock, S. A., & McCammon, J. A. (2006). Molecular dynamics: Survey of methods for simulating the activity of proteins. Chemical Reviews, 106(5), 1589–1615.CrossRef Adcock, S. A., & McCammon, J. A. (2006). Molecular dynamics: Survey of methods for simulating the activity of proteins. Chemical Reviews, 106(5), 1589–1615.CrossRef
Zurück zum Zitat Akimov, A. V., & Prezhdo, O. V. (2015). Large-scale computations in chemistry: A bird’s eye view of a vibrant field. Chemical Reviews, 115(12), 5797–5890.CrossRef Akimov, A. V., & Prezhdo, O. V. (2015). Large-scale computations in chemistry: A bird’s eye view of a vibrant field. Chemical Reviews, 115(12), 5797–5890.CrossRef
Zurück zum Zitat Aksimentiev, A., Balabin, I. A., Fillingame, R. H., & Schulten, K. (2004). Insights into the molecular mechanism of rotation in the Fo sector of ATP synthase. Biophysical Journal, 86(3), 1332–1344.CrossRef Aksimentiev, A., Balabin, I. A., Fillingame, R. H., & Schulten, K. (2004). Insights into the molecular mechanism of rotation in the Fo sector of ATP synthase. Biophysical Journal, 86(3), 1332–1344.CrossRef
Zurück zum Zitat Aksimentiev, A., Brunner, R., Cohen, J., Comer, J., Cruz-Chu, E., Hardy, D., et al. (2008). Computer modeling in biotechnology: A partner in development. Methods in Molecular Biology, 474, 181–234.CrossRef Aksimentiev, A., Brunner, R., Cohen, J., Comer, J., Cruz-Chu, E., Hardy, D., et al. (2008). Computer modeling in biotechnology: A partner in development. Methods in Molecular Biology, 474, 181–234.CrossRef
Zurück zum Zitat Alder, B. J., & Wainwright, T. E. (1957). Phase transition for a hard sphere system. The Journal of Chemical Physics, 27, 1208–1210.CrossRef Alder, B. J., & Wainwright, T. E. (1957). Phase transition for a hard sphere system. The Journal of Chemical Physics, 27, 1208–1210.CrossRef
Zurück zum Zitat Aleksandrov, A., Thompson, D., & Simonson, T. (2010). Alchemical free energy simulations for biological complexes: Powerful but temperamental. Journal of Molecular Recognition, 23(2), 117–127. Aleksandrov, A., Thompson, D., & Simonson, T. (2010). Alchemical free energy simulations for biological complexes: Powerful but temperamental. Journal of Molecular Recognition, 23(2), 117–127.
Zurück zum Zitat Alexander, S. (2010). Visualization and analysis of atomistic simulation data with OVITO–the open visualization tool. Modelling and Simulation in Materials Science and Engineering, 18(1), 015012.CrossRef Alexander, S. (2010). Visualization and analysis of atomistic simulation data with OVITO–the open visualization tool. Modelling and Simulation in Materials Science and Engineering, 18(1), 015012.CrossRef
Zurück zum Zitat Aliev, A. E., & Courtier-Murias, D. (2010). Experimental verification of force fields for molecular dynamics simulations using Gly-Pro-Gly-Gly. Journal of Physical Chemistry B, 114(38), 12358–12375.CrossRef Aliev, A. E., & Courtier-Murias, D. (2010). Experimental verification of force fields for molecular dynamics simulations using Gly-Pro-Gly-Gly. Journal of Physical Chemistry B, 114(38), 12358–12375.CrossRef
Zurück zum Zitat Allen, M. P., & Tildesley, D. J. (1987). Computer simulation of liquids. Oxford: Clarendon. Allen, M. P., & Tildesley, D. J. (1987). Computer simulation of liquids. Oxford: Clarendon.
Zurück zum Zitat Amadei, A., Linssen, A. B., & Berendsen, H. J. (1993). Essential dynamics of proteins. Proteins, 17(4), 412–425.CrossRef Amadei, A., Linssen, A. B., & Berendsen, H. J. (1993). Essential dynamics of proteins. Proteins, 17(4), 412–425.CrossRef
Zurück zum Zitat Andersen, O. J., Grouleff, J., Needham, P., Walker, R. C., & Jensen, F. (2015). Toward an enhanced sampling molecular dynamics method for studying ligand-induced conformational changes in proteins. Journal of Physical Chemistry B, 119(46), 14594–14603.CrossRef Andersen, O. J., Grouleff, J., Needham, P., Walker, R. C., & Jensen, F. (2015). Toward an enhanced sampling molecular dynamics method for studying ligand-induced conformational changes in proteins. Journal of Physical Chemistry B, 119(46), 14594–14603.CrossRef
Zurück zum Zitat Andoh, Y., Yoshii, N., Fujimoto, K., Mizutani, K., Kojima, H., Yamada, A., et al. (2013). MODYLAS: A highly parallelized general-purpose molecular dynamics simulation program for large-scale systems with long-range forces calculated by fast multipole method (FMM) and highly scalable fine-grained new parallel processing algorithms. Journal of Chemical Theory and Computation, 9(7), 3201–3209.CrossRef Andoh, Y., Yoshii, N., Fujimoto, K., Mizutani, K., Kojima, H., Yamada, A., et al. (2013). MODYLAS: A highly parallelized general-purpose molecular dynamics simulation program for large-scale systems with long-range forces calculated by fast multipole method (FMM) and highly scalable fine-grained new parallel processing algorithms. Journal of Chemical Theory and Computation, 9(7), 3201–3209.CrossRef
Zurück zum Zitat Aqvist, J., Luzhkov, V. B., & Brandsdal, B. O. (2002). Ligand binding affinities from MD simulations. Accounts of Chemical Research, 35(6), 358–365.CrossRef Aqvist, J., Luzhkov, V. B., & Brandsdal, B. O. (2002). Ligand binding affinities from MD simulations. Accounts of Chemical Research, 35(6), 358–365.CrossRef
Zurück zum Zitat Aryal, P., Sansom, M. S., & Tucker, S. J. (2015). Hydrophobic gating in ion channels. Journal of Molecular Biology, 427(1), 121–130.CrossRef Aryal, P., Sansom, M. S., & Tucker, S. J. (2015). Hydrophobic gating in ion channels. Journal of Molecular Biology, 427(1), 121–130.CrossRef
Zurück zum Zitat Avila, C. L., Drechsel, N. J., Alcantara, R., & Ville-Freixa, J. (2011). Multiscale molecular dynamics of protein aggregation. Current Protein and Peptide Science, 21, 12(3), 221–234. Avila, C. L., Drechsel, N. J., Alcantara, R., & Ville-Freixa, J. (2011). Multiscale molecular dynamics of protein aggregation. Current Protein and Peptide Science, 21, 12(3), 221–234.
Zurück zum Zitat Ayton, G. S., Noid, W. G., & Voth, G. A. (2007). Multiscale modeling of biomolecular systems: In serial and in parallel. Current Opinion in Structural Biology, 17(2), 192–198.CrossRef Ayton, G. S., Noid, W. G., & Voth, G. A. (2007). Multiscale modeling of biomolecular systems: In serial and in parallel. Current Opinion in Structural Biology, 17(2), 192–198.CrossRef
Zurück zum Zitat Ayton, G. S., Lyman, E., & Voth, G. A. (2010). Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales. Faraday Discussions, 144, 347–357.CrossRef Ayton, G. S., Lyman, E., & Voth, G. A. (2010). Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales. Faraday Discussions, 144, 347–357.CrossRef
Zurück zum Zitat Bahar, I., Lezon, T. R., Yang, L.-W., & Eyal, E. (2010). Global dynamics of proteins: Bridging between structure and function. Annual Review of Biophysics, 39(1), 23–42.CrossRef Bahar, I., Lezon, T. R., Yang, L.-W., & Eyal, E. (2010). Global dynamics of proteins: Bridging between structure and function. Annual Review of Biophysics, 39(1), 23–42.CrossRef
Zurück zum Zitat Bahar, I., Cheng, M. H., Lee, J. Y., Kaya, C., & Zhang, S. (2015). Structure-encoded global motions and their role in mediating protein-substrate interactions. Biophysical Journal, 109(6), 1101–1109.CrossRef Bahar, I., Cheng, M. H., Lee, J. Y., Kaya, C., & Zhang, S. (2015). Structure-encoded global motions and their role in mediating protein-substrate interactions. Biophysical Journal, 109(6), 1101–1109.CrossRef
Zurück zum Zitat Baker, C. M., & Best, R. B. (2013). Matching of additive and polarizable force fields for multiscale condensed phase simulations. Journal of Chemical Theory and Computation, 9(6), 2826–2837.CrossRef Baker, C. M., & Best, R. B. (2013). Matching of additive and polarizable force fields for multiscale condensed phase simulations. Journal of Chemical Theory and Computation, 9(6), 2826–2837.CrossRef
Zurück zum Zitat Baker, C. M., & Best, R. B. (2014). Insights into the binding of intrinsically disordered proteins from molecular dynamics simulation. Wiley Interdisciplinary Reviews: Computational Molecular Science, 4(3), 182–198. Baker, C. M., & Best, R. B. (2014). Insights into the binding of intrinsically disordered proteins from molecular dynamics simulation. Wiley Interdisciplinary Reviews: Computational Molecular Science, 4(3), 182–198.
Zurück zum Zitat Barnoud, J., & Monticelli, L. (2015). Coarse-grained force fields for molecular simulations. Methods in Molecular Biology, 1215, 125–149.CrossRef Barnoud, J., & Monticelli, L. (2015). Coarse-grained force fields for molecular simulations. Methods in Molecular Biology, 1215, 125–149.CrossRef
Zurück zum Zitat Beauchamp, K. A., Lin, Y. S., Das, R., & Pande, V. S. (2012). Are protein force fields getting better? A systematic benchmark on 524 diverse NMR measurements. Journal of Chemical Theory and Computation, 8(4), 1409–1414.CrossRef Beauchamp, K. A., Lin, Y. S., Das, R., & Pande, V. S. (2012). Are protein force fields getting better? A systematic benchmark on 524 diverse NMR measurements. Journal of Chemical Theory and Computation, 8(4), 1409–1414.CrossRef
Zurück zum Zitat Becker, O. M., & Karplus, M. (2006). A guide to biomolecular simulations (Vol. 4). Dordrecht: Springer. Becker, O. M., & Karplus, M. (2006). A guide to biomolecular simulations (Vol. 4). Dordrecht: Springer.
Zurück zum Zitat Becker, T., Bhushan, S., Jarasch, A., Armache, J. P., Funes, S., Jossinet, F., et al. (2009). Structure of monomeric yeast and mammalian Sec61 complexes interacting with the translating ribosome. Science, 326(5958), 1369–1373.CrossRef Becker, T., Bhushan, S., Jarasch, A., Armache, J. P., Funes, S., Jossinet, F., et al. (2009). Structure of monomeric yeast and mammalian Sec61 complexes interacting with the translating ribosome. Science, 326(5958), 1369–1373.CrossRef
Zurück zum Zitat Belden, O. S., Baker, S. C., & Baker, B. M. (2015). Citizens unite for computational immunology! Trends in Immunology, 36(7), 385–387.CrossRef Belden, O. S., Baker, S. C., & Baker, B. M. (2015). Citizens unite for computational immunology! Trends in Immunology, 36(7), 385–387.CrossRef
Zurück zum Zitat Berendsen, H. J. C. E. (1976). In Proceedings of the CECAM workshop on models for protein dynamics, Orsay. Berendsen, H. J. C. E. (1976). In Proceedings of the CECAM workshop on models for protein dynamics, Orsay.
Zurück zum Zitat Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., et al. (2000). The protein data bank. Nucleic Acids Research, 28(1), 235–242.CrossRef Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., et al. (2000). The protein data bank. Nucleic Acids Research, 28(1), 235–242.CrossRef
Zurück zum Zitat Bernardi, R. C., Melo, M. C., & Schulten, K. (2015). Enhanced sampling techniques in molecular dynamics simulations of biological systems. Biochimica et Biophysica Acta, 1850(5), 872–877.CrossRef Bernardi, R. C., Melo, M. C., & Schulten, K. (2015). Enhanced sampling techniques in molecular dynamics simulations of biological systems. Biochimica et Biophysica Acta, 1850(5), 872–877.CrossRef
Zurück zum Zitat Biarnes, X., Bongarzone, S., Vargiu, A. V., Carloni, P., & Ruggerone, P. (2011). Molecular motions in drug design: The coming age of the metadynamics method. Journal of Computer-Aided Molecular Design, 25(5), 395–402.CrossRef Biarnes, X., Bongarzone, S., Vargiu, A. V., Carloni, P., & Ruggerone, P. (2011). Molecular motions in drug design: The coming age of the metadynamics method. Journal of Computer-Aided Molecular Design, 25(5), 395–402.CrossRef
Zurück zum Zitat Bikiel, D. E., Boechi, L., Capece, L., Crespo, A., De Biase, P. M., Di Lella, S., et al. (2006). Modeling heme proteins using atomistic simulations. Physical Chemistry Chemical Physics, 8(48), 5611–5628.CrossRef Bikiel, D. E., Boechi, L., Capece, L., Crespo, A., De Biase, P. M., Di Lella, S., et al. (2006). Modeling heme proteins using atomistic simulations. Physical Chemistry Chemical Physics, 8(48), 5611–5628.CrossRef
Zurück zum Zitat Bisha, I., & Magistrato, A. (2016). The molecular mechanism of secondary sodium symporters under the lens of the computational microscope. RSC Advances, 6, 9522–9540.CrossRef Bisha, I., & Magistrato, A. (2016). The molecular mechanism of secondary sodium symporters under the lens of the computational microscope. RSC Advances, 6, 9522–9540.CrossRef
Zurück zum Zitat Blaszczyk, M., Jamroz, M., Kmiecik, S., & Kolinski, A. (2013). CABS-fold: Server for the de novo and consensus-based prediction of protein structure. Nucleic Acids Res, 41(Web Server issue), W406–411. Blaszczyk, M., Jamroz, M., Kmiecik, S., & Kolinski, A. (2013). CABS-fold: Server for the de novo and consensus-based prediction of protein structure. Nucleic Acids Res, 41(Web Server issue), W406–411.
Zurück zum Zitat Boas, F. E., & Harbury, P. B. (2007). Potential energy functions for protein design. Current Opinion in Structural Biology, 17(2), 199–204.CrossRef Boas, F. E., & Harbury, P. B. (2007). Potential energy functions for protein design. Current Opinion in Structural Biology, 17(2), 199–204.CrossRef
Zurück zum Zitat Bock, L. V., Blau, C., Schröder, G. F., Davydov, I. I., Fischer, N., Stark, H., et al. (2013). Energy barriers and driving forces in tRNA translocation through the ribosome. Nature Structural & Molecular Biology, 20(12), 1390–1396.CrossRef Bock, L. V., Blau, C., Schröder, G. F., Davydov, I. I., Fischer, N., Stark, H., et al. (2013). Energy barriers and driving forces in tRNA translocation through the ribosome. Nature Structural & Molecular Biology, 20(12), 1390–1396.CrossRef
Zurück zum Zitat Boiteux, C., Kraszewski, S., Ramseyer, C., & Girardet, C. (2007). Ion conductance vs. pore gating and selectivity in KcsA channel: Modeling achievements and perspectives. Journal of Molecular Modeling, 13(6–7), 699–713.CrossRef Boiteux, C., Kraszewski, S., Ramseyer, C., & Girardet, C. (2007). Ion conductance vs. pore gating and selectivity in KcsA channel: Modeling achievements and perspectives. Journal of Molecular Modeling, 13(6–7), 699–713.CrossRef
Zurück zum Zitat Borhani, D. W., & Shaw, D. E. (2012). The future of molecular dynamics simulations in drug discovery. Journal of Computer-Aided Molecular Design, 26(1), 15–26.CrossRef Borhani, D. W., & Shaw, D. E. (2012). The future of molecular dynamics simulations in drug discovery. Journal of Computer-Aided Molecular Design, 26(1), 15–26.CrossRef
Zurück zum Zitat Bottaro, S., Lindorff-Larsen, K., & Best, R. B. (2013). Variational optimization of an all-atom implicit solvent force field to match explicit solvent simulation data. Journal of Chemical Theory and Computation, 9(12), 5641–5652.CrossRef Bottaro, S., Lindorff-Larsen, K., & Best, R. B. (2013). Variational optimization of an all-atom implicit solvent force field to match explicit solvent simulation data. Journal of Chemical Theory and Computation, 9(12), 5641–5652.CrossRef
Zurück zum Zitat Bowman, G. R., Voelz, V. A., & Pande, V. S. (2011). Taming the complexity of protein folding. Current Opinion in Structural Biology, 21(1), 4–11.CrossRef Bowman, G. R., Voelz, V. A., & Pande, V. S. (2011). Taming the complexity of protein folding. Current Opinion in Structural Biology, 21(1), 4–11.CrossRef
Zurück zum Zitat Brooks, B. R., Brooks, C. L., 3rd, Mackerell, A. D., Jr., Nilsson, L., Petrella, R. J., Roux, B., et al. (2009). CHARMM: The biomolecular simulation program. Journal of Computational Chemistry, 30(10), 1545–1614.CrossRef Brooks, B. R., Brooks, C. L., 3rd, Mackerell, A. D., Jr., Nilsson, L., Petrella, R. J., Roux, B., et al. (2009). CHARMM: The biomolecular simulation program. Journal of Computational Chemistry, 30(10), 1545–1614.CrossRef
Zurück zum Zitat Brunk, E., & Rothlisberger, U. (2015). Mixed quantum mechanical/molecular mechanical molecular dynamics simulations of biological systems in ground and electronically excited states. Chemical Reviews, 115(12), 6217–6263.CrossRef Brunk, E., & Rothlisberger, U. (2015). Mixed quantum mechanical/molecular mechanical molecular dynamics simulations of biological systems in ground and electronically excited states. Chemical Reviews, 115(12), 6217–6263.CrossRef
Zurück zum Zitat Carnevale, V., Raugei, S., Neri, M., Pantano, S., Micheletti, C., & Carloni, P. (2009). Multi-scale modeling of HIV-1 proteins. Journal of Molecular Structure (THEOCHEM), 898(1–3), 97–105.CrossRef Carnevale, V., Raugei, S., Neri, M., Pantano, S., Micheletti, C., & Carloni, P. (2009). Multi-scale modeling of HIV-1 proteins. Journal of Molecular Structure (THEOCHEM), 898(1–3), 97–105.CrossRef
Zurück zum Zitat Carvalho, A. T. P., Barrozo, A., Doron, D., Kilshtain, A. V., Major, D. T., & Kamerlin, S. C. L. (2014). Challenges in computational studies of enzyme structure, function and dynamics. Journal of Molecular Graphics and Modelling, 54, 62–79.CrossRef Carvalho, A. T. P., Barrozo, A., Doron, D., Kilshtain, A. V., Major, D. T., & Kamerlin, S. C. L. (2014). Challenges in computational studies of enzyme structure, function and dynamics. Journal of Molecular Graphics and Modelling, 54, 62–79.CrossRef
Zurück zum Zitat Case, D. A., Cheatham, T. E., 3rd, Darden, T., Gohlke, H., Luo, R., Merz, K. M., Jr., et al. (2005). The Amber biomolecular simulation programs. Journal of Computational Chemistry, 26(16), 1668–1688.CrossRef Case, D. A., Cheatham, T. E., 3rd, Darden, T., Gohlke, H., Luo, R., Merz, K. M., Jr., et al. (2005). The Amber biomolecular simulation programs. Journal of Computational Chemistry, 26(16), 1668–1688.CrossRef
Zurück zum Zitat Chen, J., & Brooks, C. L., 3rd. (2008). Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions. Physical Chemistry Chemical Physics, 10(4), 471–481.CrossRef Chen, J., & Brooks, C. L., 3rd. (2008). Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions. Physical Chemistry Chemical Physics, 10(4), 471–481.CrossRef
Zurück zum Zitat Chen, J., Brooks, C. L., 3rd, & Khandogin, J. (2008). Recent advances in implicit solvent-based methods for biomolecular simulations. Current Opinion in Structural Biology, 18(2), 140–148.CrossRef Chen, J., Brooks, C. L., 3rd, & Khandogin, J. (2008). Recent advances in implicit solvent-based methods for biomolecular simulations. Current Opinion in Structural Biology, 18(2), 140–148.CrossRef
Zurück zum Zitat Chen, J., Xie, Z. -R., & Wu, Y. (2016). Study of protein structural deformations under external mechanical perturbations by a coarse-grained simulation method. Biomechanics and Modeling in Mechanobiology, 15, 317–329. Chen, J., Xie, Z. -R., & Wu, Y. (2016). Study of protein structural deformations under external mechanical perturbations by a coarse-grained simulation method. Biomechanics and Modeling in Mechanobiology, 15, 317–329.
Zurück zum Zitat Chipot, C. (2015). Applications to real size biological systems. In B. Engquist (Ed.), Encyclopedia of applied and computational mathematics (pp. 72–81). Berlin/Heidelberg: Springer.CrossRef Chipot, C. (2015). Applications to real size biological systems. In B. Engquist (Ed.), Encyclopedia of applied and computational mathematics (pp. 72–81). Berlin/Heidelberg: Springer.CrossRef
Zurück zum Zitat Chou, K. C. (2004). Structural bioinformatics and its impact to biomedical science. Current Medicinal Chemistry, 11(16), 2105–2134.CrossRef Chou, K. C. (2004). Structural bioinformatics and its impact to biomedical science. Current Medicinal Chemistry, 11(16), 2105–2134.CrossRef
Zurück zum Zitat Christ, C. D., Mark, A. E., & van Gunsteren, W. F. (2010). Basic ingredients of free energy calculations: A review. Journal of Computational Chemistry, 31(8), 1569–1582. Christ, C. D., Mark, A. E., & van Gunsteren, W. F. (2010). Basic ingredients of free energy calculations: A review. Journal of Computational Chemistry, 31(8), 1569–1582.
Zurück zum Zitat Christen, M., Hunenberger, P. H., Bakowies, D., Baron, R., Burgi, R., Geerke, D. P., et al. (2005). The GROMOS software for biomolecular simulation: GROMOS05. Journal of Computational Chemistry, 26(16), 1719–1751.CrossRef Christen, M., Hunenberger, P. H., Bakowies, D., Baron, R., Burgi, R., Geerke, D. P., et al. (2005). The GROMOS software for biomolecular simulation: GROMOS05. Journal of Computational Chemistry, 26(16), 1719–1751.CrossRef
Zurück zum Zitat Chu, J.-W., Ayton, G. S., Izvekov, S., & Voth, G. A. (2007). Emerging methods for multiscale simulation of biomolecular systems. Molecular Physics, 105, 167–175.CrossRef Chu, J.-W., Ayton, G. S., Izvekov, S., & Voth, G. A. (2007). Emerging methods for multiscale simulation of biomolecular systems. Molecular Physics, 105, 167–175.CrossRef
Zurück zum Zitat Chwastyk, M., Galera-Prat, A., Sikora, M., Gomez-Sicilia, A., Carrion-Vazquez, M., & Cieplak, M. (2014). Theoretical tests of the mechanical protection strategy in protein nanomechanics. Proteins, 82(5), 717–726.CrossRef Chwastyk, M., Galera-Prat, A., Sikora, M., Gomez-Sicilia, A., Carrion-Vazquez, M., & Cieplak, M. (2014). Theoretical tests of the mechanical protection strategy in protein nanomechanics. Proteins, 82(5), 717–726.CrossRef
Zurück zum Zitat Clementi, C. (2008). Coarse-grained models of protein folding: Toy models or predictive tools? Current Opinion in Structural Biology, 18(1), 10–15.CrossRef Clementi, C. (2008). Coarse-grained models of protein folding: Toy models or predictive tools? Current Opinion in Structural Biology, 18(1), 10–15.CrossRef
Zurück zum Zitat Cohen, J., Olsen, K. W., & Schulten, K. (2008). Finding gas migration pathways in proteins using implicit ligand sampling. Methods in Enzymology, 437, 439–457.CrossRef Cohen, J., Olsen, K. W., & Schulten, K. (2008). Finding gas migration pathways in proteins using implicit ligand sampling. Methods in Enzymology, 437, 439–457.CrossRef
Zurück zum Zitat Comer, J., Phillips, J. C., Schulten, K., & Chipot, C. (2014). Multiple-replica strategies for free-energy calculations in NAMD: Multiple-walker adaptive biasing force and walker selection rules. Journal of Chemical Theory and Computation, 10(12), 5276–5285.CrossRef Comer, J., Phillips, J. C., Schulten, K., & Chipot, C. (2014). Multiple-replica strategies for free-energy calculations in NAMD: Multiple-walker adaptive biasing force and walker selection rules. Journal of Chemical Theory and Computation, 10(12), 5276–5285.CrossRef
Zurück zum Zitat Cornell, W., & Nam, K. (2009). Steroid hormone binding receptors: Application of homology modeling, induced fit docking, and molecular dynamics to study structure-function relationships. Current Topics in Medicinal Chemistry, 9(9), 844–853.CrossRef Cornell, W., & Nam, K. (2009). Steroid hormone binding receptors: Application of homology modeling, induced fit docking, and molecular dynamics to study structure-function relationships. Current Topics in Medicinal Chemistry, 9(9), 844–853.CrossRef
Zurück zum Zitat Cumberworth, A., Bui, J. M., & Gsponer, J. (2015). Free energies of solvation in the context of protein folding: Implications for implicit and explicit solvent models. Journal of Computational Chemistry, 37(7), 629–640.CrossRef Cumberworth, A., Bui, J. M., & Gsponer, J. (2015). Free energies of solvation in the context of protein folding: Implications for implicit and explicit solvent models. Journal of Computational Chemistry, 37(7), 629–640.CrossRef
Zurück zum Zitat Czub, J., & Grubmuller, H. (2014). Rotation triggers nucleotide-independent conformational transition of the empty beta subunit of F(1)-ATPase. Journal of the American Chemical Society, 136(19), 6960–6968.CrossRef Czub, J., & Grubmuller, H. (2014). Rotation triggers nucleotide-independent conformational transition of the empty beta subunit of F(1)-ATPase. Journal of the American Chemical Society, 136(19), 6960–6968.CrossRef
Zurück zum Zitat Dahl, J. P. (2001). Introduction to the quantum world of atoms and molecules. Singapore: World Scientific.CrossRef Dahl, J. P. (2001). Introduction to the quantum world of atoms and molecules. Singapore: World Scientific.CrossRef
Zurück zum Zitat Dal Peraro, M., Ruggerone, P., Raugei, S., Gervasi, F., & Elber, R. (2005). Long-timescale simulation methods. Current Opinion in Structural Biology, 15, 151–156.CrossRef Dal Peraro, M., Ruggerone, P., Raugei, S., Gervasi, F., & Elber, R. (2005). Long-timescale simulation methods. Current Opinion in Structural Biology, 15, 151–156.CrossRef
Zurück zum Zitat Dal Peraro, M., Ruggerone, P., Raugei, S., Gervasio, F. L., & Carloni, P. (2007). Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations. Current Opinion in Structural Biology, 17(2), 149–156.CrossRef Dal Peraro, M., Ruggerone, P., Raugei, S., Gervasio, F. L., & Carloni, P. (2007). Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations. Current Opinion in Structural Biology, 17(2), 149–156.CrossRef
Zurück zum Zitat Damborsky, J., & Brezovsky, J. (2014). Computational tools for designing and engineering enzymes. Current Opinion in Chemical Biology, 19, 8–16.CrossRef Damborsky, J., & Brezovsky, J. (2014). Computational tools for designing and engineering enzymes. Current Opinion in Chemical Biology, 19, 8–16.CrossRef
Zurück zum Zitat DeLano, W. L. (2002). The PyMOL molecular graphics system. DeLano, W. L. (2002). The PyMOL molecular graphics system.
Zurück zum Zitat Delemotte, L., Kasimova, M. A., Klein, M. L., Tarek, M., & Carnevale, V. (2015). Free-energy landscape of ion-channel voltage-sensor–domain activation. Proceedings of the National Academy of Sciences, 112(1), 124–129.CrossRef Delemotte, L., Kasimova, M. A., Klein, M. L., Tarek, M., & Carnevale, V. (2015). Free-energy landscape of ion-channel voltage-sensor–domain activation. Proceedings of the National Academy of Sciences, 112(1), 124–129.CrossRef
Zurück zum Zitat DeMarco, M. L., & Daggett, V. (2009). Characterization of cell-surface prion protein relative to its recombinant analogue: Insights from molecular dynamics simulations of diglycosylated, membrane-bound human prion protein. Journal of Neurochemistry, 109(1), 60–73.CrossRef DeMarco, M. L., & Daggett, V. (2009). Characterization of cell-surface prion protein relative to its recombinant analogue: Insights from molecular dynamics simulations of diglycosylated, membrane-bound human prion protein. Journal of Neurochemistry, 109(1), 60–73.CrossRef
Zurück zum Zitat Deng, Y., & Roux, B. (2009). Computations of standard binding free energies with molecular dynamics simulations. Journal of Physical Chemistry B, 113(8), 2234–2246.CrossRef Deng, Y., & Roux, B. (2009). Computations of standard binding free energies with molecular dynamics simulations. Journal of Physical Chemistry B, 113(8), 2234–2246.CrossRef
Zurück zum Zitat Di Marino, D., Bonome, E. L., Tramontano, A., & Chinappi, M. (2015). All-atom molecular dynamics simulation of protein translocation through an α-hemolysin nanopore. Journal of Physical Chemistry Letters, 6(15), 2963–2968.CrossRef Di Marino, D., Bonome, E. L., Tramontano, A., & Chinappi, M. (2015). All-atom molecular dynamics simulation of protein translocation through an α-hemolysin nanopore. Journal of Physical Chemistry Letters, 6(15), 2963–2968.CrossRef
Zurück zum Zitat Dill, K. A., & MacCallum, J. L. (2012). The protein-folding problem, 50 years on. Science, 338(6110), 1042–1046.CrossRef Dill, K. A., & MacCallum, J. L. (2012). The protein-folding problem, 50 years on. Science, 338(6110), 1042–1046.CrossRef
Zurück zum Zitat Dittrich, M., & Schulten, K. (2006). PcrA helicase, a prototype ATP-driven molecular motor. Structure, 14(9), 1345–1353.CrossRef Dittrich, M., & Schulten, K. (2006). PcrA helicase, a prototype ATP-driven molecular motor. Structure, 14(9), 1345–1353.CrossRef
Zurück zum Zitat Dittrich, M., Freddolino, P. L., & Schulten, K. (2005). When light falls in LOV: A quantum mechanical/molecular mechanical study of photoexcitation in Phot-LOV1 of Chlamydomonas reinhardtii. Journal of Physical Chemistry B, 109(26), 13006–13013.CrossRef Dittrich, M., Freddolino, P. L., & Schulten, K. (2005). When light falls in LOV: A quantum mechanical/molecular mechanical study of photoexcitation in Phot-LOV1 of Chlamydomonas reinhardtii. Journal of Physical Chemistry B, 109(26), 13006–13013.CrossRef
Zurück zum Zitat Do, T. N., Choy, W. Y., & Karttunen, M. (2014). Accelerating the conformational sampling of intrinsically disordered proteins. Journal of Chemical Theory and Computation, 10(11),5081–5094.CrossRef Do, T. N., Choy, W. Y., & Karttunen, M. (2014). Accelerating the conformational sampling of intrinsically disordered proteins. Journal of Chemical Theory and Computation, 10(11),5081–5094.CrossRef
Zurück zum Zitat Dodson, G. G., Lane, D. P., & Verma, C. S. (2008). Molecular simulations of protein dynamics: New windows on mechanisms in biology. EMBO Reports, 9(2), 144–150.CrossRef Dodson, G. G., Lane, D. P., & Verma, C. S. (2008). Molecular simulations of protein dynamics: New windows on mechanisms in biology. EMBO Reports, 9(2), 144–150.CrossRef
Zurück zum Zitat Dror, R. O., Dirks, R. M., Grossman, J. P., Xu, H. F., & Shaw, D. E. (2012). Biomolecular simulation: A computational microscope for molecular biology. Annual Review of Biophysics, 41(41), 429–452.CrossRef Dror, R. O., Dirks, R. M., Grossman, J. P., Xu, H. F., & Shaw, D. E. (2012). Biomolecular simulation: A computational microscope for molecular biology. Annual Review of Biophysics, 41(41), 429–452.CrossRef
Zurück zum Zitat Dror, R. O., Green, H. F., Valant, C., Borhani, D. W., Valcourt, J. R., Pan, A. C., et al. (2013). Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs. Nature, 503(7475), 295–299. Dror, R. O., Green, H. F., Valant, C., Borhani, D. W., Valcourt, J. R., Pan, A. C., et al. (2013). Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs. Nature, 503(7475), 295–299.
Zurück zum Zitat Duan, Y., & Kollman, P. A. (1998). Pathways to a protein folding intermediate observed in a1-microsecond simulation in aqueous solution. Science, 282(5389), 740–744.CrossRef Duan, Y., & Kollman, P. A. (1998). Pathways to a protein folding intermediate observed in a1-microsecond simulation in aqueous solution. Science, 282(5389), 740–744.CrossRef
Zurück zum Zitat Eastman, P., & Pande, V. S. (2015). OpenMM: A hardware independent framework for molecular simulations. Computing in Science & Engineering, 12(4), 34–39.CrossRef Eastman, P., & Pande, V. S. (2015). OpenMM: A hardware independent framework for molecular simulations. Computing in Science & Engineering, 12(4), 34–39.CrossRef
Zurück zum Zitat Elber, R. (2010). Ligand diffusion in globins: Simulations versus experiment. Current Opinion in Structural Biology, 20(2), 162–167.CrossRef Elber, R. (2010). Ligand diffusion in globins: Simulations versus experiment. Current Opinion in Structural Biology, 20(2), 162–167.CrossRef
Zurück zum Zitat Elber, R., & Kirmizialtin, S. (2013). Molecular machines. Current Opinion in Structural Biology, 23(2), 206–211.CrossRef Elber, R., & Kirmizialtin, S. (2013). Molecular machines. Current Opinion in Structural Biology, 23(2), 206–211.CrossRef
Zurück zum Zitat Elber, R., Ghosh, A., & Cardenas, A. (2002). Long time dynamics of complex systems. Accounts of Chemical Research, 35(6), 396–403.CrossRef Elber, R., Ghosh, A., & Cardenas, A. (2002). Long time dynamics of complex systems. Accounts of Chemical Research, 35(6), 396–403.CrossRef
Zurück zum Zitat English, N. J., & Waldron, C. J. (2015). Perspectives on external electric fields in molecular simulation: Progress, prospects and challenges. Physical Chemistry Chemical Physics, 17(19), 12407–12440. doi:10.1039/C5CP00629E.CrossRef English, N. J., & Waldron, C. J. (2015). Perspectives on external electric fields in molecular simulation: Progress, prospects and challenges. Physical Chemistry Chemical Physics, 17(19), 12407–12440. doi:10.1039/C5CP00629E.CrossRef
Zurück zum Zitat Ensign, D. L., Kasson, P. M., & Pande, V. S. (2007). Heterogeneity even at the speed limit of folding: Large-scale molecular dynamics study of a fast-folding variant of the villin headpiece. Journal of Molecular Biology, 374(3), 806–816.CrossRef Ensign, D. L., Kasson, P. M., & Pande, V. S. (2007). Heterogeneity even at the speed limit of folding: Large-scale molecular dynamics study of a fast-folding variant of the villin headpiece. Journal of Molecular Biology, 374(3), 806–816.CrossRef
Zurück zum Zitat Espinoza-Fonseca, L. M., & Ramírez-Salinas, G. L. (2015). Microsecond molecular simulations reveal a transient proton pathway in the calcium pump. Journal of the American Chemical Society, 137(22), 7055–7058.CrossRef Espinoza-Fonseca, L. M., & Ramírez-Salinas, G. L. (2015). Microsecond molecular simulations reveal a transient proton pathway in the calcium pump. Journal of the American Chemical Society, 137(22), 7055–7058.CrossRef
Zurück zum Zitat Estarellas, C., Otyepka, M., Koča, J., Banáš, P., Krepl, M., & Šponer, J. (2015). Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease. Biochimica et Biophysica Acta (BBA) - General Subjects, 1850(5), 1072–1090.CrossRef Estarellas, C., Otyepka, M., Koča, J., Banáš, P., Krepl, M., & Šponer, J. (2015). Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease. Biochimica et Biophysica Acta (BBA) - General Subjects, 1850(5), 1072–1090.CrossRef
Zurück zum Zitat Fersht, A. R., & Daggett, V. (2002). Protein folding and unfolding at atomic resolution. Cell, 108(4), 573–582. Fersht, A. R., & Daggett, V. (2002). Protein folding and unfolding at atomic resolution. Cell, 108(4), 573–582.
Zurück zum Zitat Field, M. J. (2015). Technical advances in molecular simulation since the 1980s. Archives of Biochemistry and Biophysics, 582, 3–9.CrossRef Field, M. J. (2015). Technical advances in molecular simulation since the 1980s. Archives of Biochemistry and Biophysics, 582, 3–9.CrossRef
Zurück zum Zitat Flechsig, H., & Mikhailov, A. S. (2010). Tracing entire operation cycles of molecular motor hepatitis C virus helicase in structurally resolved dynamical simulations. Proceedings of the National Academy of Sciences of the United States of America, 107(49), 20875–20880.CrossRef Flechsig, H., & Mikhailov, A. S. (2010). Tracing entire operation cycles of molecular motor hepatitis C virus helicase in structurally resolved dynamical simulations. Proceedings of the National Academy of Sciences of the United States of America, 107(49), 20875–20880.CrossRef
Zurück zum Zitat Forti, F., Boechi, L., Bikiel, D., Martí, M. A., Nardini, M., Bolognesi, M., et al. (2011a). Ligand migration in Methanosarcina acetivorans protoglobin: Effects of ligand binding and dimeric assembly. The Journal of Physical Chemistry B, 115(46), 13771–13780.CrossRef Forti, F., Boechi, L., Bikiel, D., Martí, M. A., Nardini, M., Bolognesi, M., et al. (2011a). Ligand migration in Methanosarcina acetivorans protoglobin: Effects of ligand binding and dimeric assembly. The Journal of Physical Chemistry B, 115(46), 13771–13780.CrossRef
Zurück zum Zitat Forti, F., Boechi, L., Estrin, D. A., & Marti, M. A. (2011b). Comparing and combining implicit ligand sampling with multiple steered molecular dynamics to study ligand migration processes in heme proteins. Journal of Computational Chemistry, 32(10), 2219–2231.CrossRef Forti, F., Boechi, L., Estrin, D. A., & Marti, M. A. (2011b). Comparing and combining implicit ligand sampling with multiple steered molecular dynamics to study ligand migration processes in heme proteins. Journal of Computational Chemistry, 32(10), 2219–2231.CrossRef
Zurück zum Zitat Fowler, P. W., & Sansom, M. S. (2013). The pore of voltage-gated potassium ion channels is strained when closed. Nature Communications, 4, 1872.CrossRef Fowler, P. W., & Sansom, M. S. (2013). The pore of voltage-gated potassium ion channels is strained when closed. Nature Communications, 4, 1872.CrossRef
Zurück zum Zitat Frankel, D., & Smit, B. (2001). Understanding molecular simulation (2nd ed.). San Diego: Academic. Frankel, D., & Smit, B. (2001). Understanding molecular simulation (2nd ed.). San Diego: Academic.
Zurück zum Zitat Freddolino, P. L., & Schulten, K. (2009). Common structural transitions in explicit-solvent simulations of villin headpiece folding. Biophysical Journal, 97(8), 2338–2347.CrossRef Freddolino, P. L., & Schulten, K. (2009). Common structural transitions in explicit-solvent simulations of villin headpiece folding. Biophysical Journal, 97(8), 2338–2347.CrossRef
Zurück zum Zitat Freddolino, P. L., Arkhipov, A. S., Larson, S. B., McPherson, A., & Schulten, K. (2006a). Molecular dynamics simulations of the complete satellite tobacco mosaic virus. Structure, 14(3), 437–449.CrossRef Freddolino, P. L., Arkhipov, A. S., Larson, S. B., McPherson, A., & Schulten, K. (2006a). Molecular dynamics simulations of the complete satellite tobacco mosaic virus. Structure, 14(3), 437–449.CrossRef
Zurück zum Zitat Freddolino, P. L., Dittrich, M., & Schulten, K. (2006b). Dynamic switching mechanisms in LOV1 and LOV2 domains of plant phototropins. Biophysical Journal, 91(10), 3630–3639.CrossRef Freddolino, P. L., Dittrich, M., & Schulten, K. (2006b). Dynamic switching mechanisms in LOV1 and LOV2 domains of plant phototropins. Biophysical Journal, 91(10), 3630–3639.CrossRef
Zurück zum Zitat Freddolino, P. L., Liu, F., Gruebele, M., & Schulten, K. (2008). Ten-microsecond molecular dynamics simulation of a fast-folding WW domain. Biophysical Journal, 94(10), L75–77.CrossRef Freddolino, P. L., Liu, F., Gruebele, M., & Schulten, K. (2008). Ten-microsecond molecular dynamics simulation of a fast-folding WW domain. Biophysical Journal, 94(10), L75–77.CrossRef
Zurück zum Zitat Freddolino, P. L., Harrison, C. B., Liu, Y., & Schulten, K. (2010). Challenges in protein folding simulations: Timescale, representation, and analysis. Nature Physics, 6(10), 751–758.CrossRef Freddolino, P. L., Harrison, C. B., Liu, Y., & Schulten, K. (2010). Challenges in protein folding simulations: Timescale, representation, and analysis. Nature Physics, 6(10), 751–758.CrossRef
Zurück zum Zitat Frenkel, D., & Smit, B. (2002). Chapter 4 – Molecular dynamics simulations. In Understanding molecular simulation (2nd ed., pp. 63–107). San Diego: Academic.CrossRef Frenkel, D., & Smit, B. (2002). Chapter 4 – Molecular dynamics simulations. In Understanding molecular simulation (2nd ed., pp. 63–107). San Diego: Academic.CrossRef
Zurück zum Zitat Fu, B., & Vendruscolo, M. (2015). Structure and dynamics of intrinsically disordered proteins. Advances in Experimental Medicine and Biology, 870, 35–48.CrossRef Fu, B., & Vendruscolo, M. (2015). Structure and dynamics of intrinsically disordered proteins. Advances in Experimental Medicine and Biology, 870, 35–48.CrossRef
Zurück zum Zitat Fujisaki, H., Moritsugu, K., Matsunaga, Y., Morishita, T., & Maragliano, L. (2015). Extended phase-space methods for enhanced sampling in molecular simulations: A review. Frontiers in Bioengineering and Biotechnology, 3, 125.CrossRef Fujisaki, H., Moritsugu, K., Matsunaga, Y., Morishita, T., & Maragliano, L. (2015). Extended phase-space methods for enhanced sampling in molecular simulations: A review. Frontiers in Bioengineering and Biotechnology, 3, 125.CrossRef
Zurück zum Zitat Furini, S., Domene, C., & Cavalcanti, S. (2010). Insights into the sliding movement of the lac repressor nonspecifically bound to DNA. The Journal of Physical Chemistry B, 114(6), 2238–2245.CrossRef Furini, S., Domene, C., & Cavalcanti, S. (2010). Insights into the sliding movement of the lac repressor nonspecifically bound to DNA. The Journal of Physical Chemistry B, 114(6), 2238–2245.CrossRef
Zurück zum Zitat Galeazzi, R. (2009). Molecular dynamics as a tool in rational drug design: Current status and some major applications. Current Computer-Aided Drug Design, 5(4), 225–240.CrossRef Galeazzi, R. (2009). Molecular dynamics as a tool in rational drug design: Current status and some major applications. Current Computer-Aided Drug Design, 5(4), 225–240.CrossRef
Zurück zum Zitat Galera-Prat, A., Gomez-Sicilia, A., Oberhauser, A. F., Cieplak, M., & Carrion-Vazquez, M. (2010). Understanding biology by stretching proteins: Recent progress. Current Opinion in Structural Biology, 20(1), 63–69.CrossRef Galera-Prat, A., Gomez-Sicilia, A., Oberhauser, A. F., Cieplak, M., & Carrion-Vazquez, M. (2010). Understanding biology by stretching proteins: Recent progress. Current Opinion in Structural Biology, 20(1), 63–69.CrossRef
Zurück zum Zitat Gallicchio, E., & Levy, R. M. (2011). Advances in all atom sampling methods for modeling protein-ligand binding affinities. Current Opinion in Structural Biology, 21, 161–166CrossRef Gallicchio, E., & Levy, R. M. (2011). Advances in all atom sampling methods for modeling protein-ligand binding affinities. Current Opinion in Structural Biology, 21, 161–166CrossRef
Zurück zum Zitat Gamini, R., Han, W., Stone, J. E., & Schulten, K. (2014). Assembly of Nsp1 nucleoporins provides insight into nuclear pore complex gating. PLoS Computational Biology, 10(3), e1003488.CrossRef Gamini, R., Han, W., Stone, J. E., & Schulten, K. (2014). Assembly of Nsp1 nucleoporins provides insight into nuclear pore complex gating. PLoS Computational Biology, 10(3), e1003488.CrossRef
Zurück zum Zitat Gamiz-Hernandez, A. P., & Kaila, V. R. (2016). Conversion of light-energy into molecular strain in the photocycle of the photoactive yellow protein. Physical Chemistry Chemical Physics, 18(4), 2802–2809.CrossRef Gamiz-Hernandez, A. P., & Kaila, V. R. (2016). Conversion of light-energy into molecular strain in the photocycle of the photoactive yellow protein. Physical Chemistry Chemical Physics, 18(4), 2802–2809.CrossRef
Zurück zum Zitat Gao, M., Sotomayor, M., Villa, E., Lee, E. H., & Schulten, K. (2006). Molecular mechanisms of cellular mechanics. Physical Chemistry Chemical Physics, 8(32), 3692–3706.CrossRef Gao, M., Sotomayor, M., Villa, E., Lee, E. H., & Schulten, K. (2006). Molecular mechanisms of cellular mechanics. Physical Chemistry Chemical Physics, 8(32), 3692–3706.CrossRef
Zurück zum Zitat Goga, N., Melo, M., Rzepiela, A., De Vries, A., Hadar, A., Marrink, S., et al. (2015). Benchmark of schemes for multiscale molecular dynamics simulations. Journal of Chemical Theory and Computation, 11(4), 1389–1398.CrossRef Goga, N., Melo, M., Rzepiela, A., De Vries, A., Hadar, A., Marrink, S., et al. (2015). Benchmark of schemes for multiscale molecular dynamics simulations. Journal of Chemical Theory and Computation, 11(4), 1389–1398.CrossRef
Zurück zum Zitat Goh, B. C., Perilla, J. R., England, M. R., Heyrana, K. J., Craven, R. C., & Schulten, K. (2015). Atomic modeling of an immature retroviral lattice using molecular dynamics and mutagenesis. Structure, 23(8), 1414–1425.CrossRef Goh, B. C., Perilla, J. R., England, M. R., Heyrana, K. J., Craven, R. C., & Schulten, K. (2015). Atomic modeling of an immature retroviral lattice using molecular dynamics and mutagenesis. Structure, 23(8), 1414–1425.CrossRef
Zurück zum Zitat Granata, D., Camilloni, C., Vendruscolo, M., & Laio, A. (2013). Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics. Proceedings of the National Academy of Sciences of the United States of America, 110(17), 6817–6822.CrossRef Granata, D., Camilloni, C., Vendruscolo, M., & Laio, A. (2013). Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics. Proceedings of the National Academy of Sciences of the United States of America, 110(17), 6817–6822.CrossRef
Zurück zum Zitat Granata, D., Baftizadeh, F., Habchi, J., Galvagnion, C., De Simone, A., Camilloni, C., et al. (2015). The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments. Scientific Reports, 5, 15449.CrossRef Granata, D., Baftizadeh, F., Habchi, J., Galvagnion, C., De Simone, A., Camilloni, C., et al. (2015). The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments. Scientific Reports, 5, 15449.CrossRef
Zurück zum Zitat Greenberger, D., Hentschel, K., & Weinert, F. (2009). Compendium of quantum physics. Berlin/Heidelberg: Springer.CrossRef Greenberger, D., Hentschel, K., & Weinert, F. (2009). Compendium of quantum physics. Berlin/Heidelberg: Springer.CrossRef
Zurück zum Zitat Gu, J., & Bourne, P. E. (Eds.). (2009). Structural bioinformatics (2nd ed.). Hoboken: Wiley-Blackwell. Gu, J., & Bourne, P. E. (Eds.). (2009). Structural bioinformatics (2nd ed.). Hoboken: Wiley-Blackwell.
Zurück zum Zitat Gumbart, J., Wang, Y., Aksimentiev, A., Tajkhorshid, E., & Schulten, K. (2005). Molecular dynamics simulations of proteins in lipid bilayers. Current Opinion in Structural Biology, 15(4), 423–431.CrossRef Gumbart, J., Wang, Y., Aksimentiev, A., Tajkhorshid, E., & Schulten, K. (2005). Molecular dynamics simulations of proteins in lipid bilayers. Current Opinion in Structural Biology, 15(4), 423–431.CrossRef
Zurück zum Zitat Guvench, O., & MacKerell, A. D., Jr. (2008). Comparison of protein force fields for molecular dynamics simulations. Methods in Molecular Biology, 443, 63–88.CrossRef Guvench, O., & MacKerell, A. D., Jr. (2008). Comparison of protein force fields for molecular dynamics simulations. Methods in Molecular Biology, 443, 63–88.CrossRef
Zurück zum Zitat Haile, M. (1992). Molecular dynamics simulation: Elementary methods. New York: Wiley. Haile, M. (1992). Molecular dynamics simulation: Elementary methods. New York: Wiley.
Zurück zum Zitat Hansson, T., Oostenbrink, C., & van Gunsteren, W. (2002). Molecular dynamics simulations. Current Opinion in Structural Biology, 12(2), 190–196.CrossRef Hansson, T., Oostenbrink, C., & van Gunsteren, W. (2002). Molecular dynamics simulations. Current Opinion in Structural Biology, 12(2), 190–196.CrossRef
Zurück zum Zitat Hanwell, M. D., Curtis, D. E., Lonie, D. C., Vandermeersch, T., Zurek, E., & Hutchison, G. R. (2012). Avogadro: An advanced semantic chemical editor, visualization, and analysis platform. Journal of Cheminformatics, 4(1), 17.CrossRef Hanwell, M. D., Curtis, D. E., Lonie, D. C., Vandermeersch, T., Zurek, E., & Hutchison, G. R. (2012). Avogadro: An advanced semantic chemical editor, visualization, and analysis platform. Journal of Cheminformatics, 4(1), 17.CrossRef
Zurück zum Zitat Hardy, D. J., Stone, J. E., & Schulten, K. (2009). Multilevel summation of electrostatic potentials using graphics processing units. Parallel Computing, 35(3), 164–177.CrossRef Hardy, D. J., Stone, J. E., & Schulten, K. (2009). Multilevel summation of electrostatic potentials using graphics processing units. Parallel Computing, 35(3), 164–177.CrossRef
Zurück zum Zitat Harvey, M. J., & De Fabritiis, G. (2012). High-throughput molecular dynamics: The powerful new tool for drug discovery. Drug Discovery Today, 17(19), 1059–1062.CrossRef Harvey, M. J., & De Fabritiis, G. (2012). High-throughput molecular dynamics: The powerful new tool for drug discovery. Drug Discovery Today, 17(19), 1059–1062.CrossRef
Zurück zum Zitat Hayashi, S., Tajkhorshid, E., & Schulten, K. (2009). Photochemical reaction dynamics of the primary event of vision studied by means of a hybrid molecular simulation. Biophysical Journal, 96(2), 403–416.CrossRef Hayashi, S., Tajkhorshid, E., & Schulten, K. (2009). Photochemical reaction dynamics of the primary event of vision studied by means of a hybrid molecular simulation. Biophysical Journal, 96(2), 403–416.CrossRef
Zurück zum Zitat He, C., Genchev, G. Z., Lu, H., & Li, H. (2012). Mechanically untying a protein slipknot: Multiple pathways revealed by force spectroscopy and steered molecular dynamics simulations. Journal of the American Chemical Society, 134(25), 10428–10435.CrossRef He, C., Genchev, G. Z., Lu, H., & Li, H. (2012). Mechanically untying a protein slipknot: Multiple pathways revealed by force spectroscopy and steered molecular dynamics simulations. Journal of the American Chemical Society, 134(25), 10428–10435.CrossRef
Zurück zum Zitat Hensen, U., Meyer, T., Haas, J., Rex, R., Vriend, G., & Grubmuller, H. (2012). Exploring protein dynamics space: The dynasome as the missing link between protein structure and function. PLoS One, 7(5), e33931.CrossRef Hensen, U., Meyer, T., Haas, J., Rex, R., Vriend, G., & Grubmuller, H. (2012). Exploring protein dynamics space: The dynasome as the missing link between protein structure and function. PLoS One, 7(5), e33931.CrossRef
Zurück zum Zitat Henzler-Wildman, K., & Kern, D. (2007). Dynamic personalities of proteins. Nature, 450(7172), 964–972.CrossRef Henzler-Wildman, K., & Kern, D. (2007). Dynamic personalities of proteins. Nature, 450(7172), 964–972.CrossRef
Zurück zum Zitat Horn, R., Roux, B., & Aqvist, J. (2014). Permeation redux: Thermodynamics and kinetics of ion movement through potassium channels. Biophysical Journal, 106(9), 1859–1863.CrossRef Horn, R., Roux, B., & Aqvist, J. (2014). Permeation redux: Thermodynamics and kinetics of ion movement through potassium channels. Biophysical Journal, 106(9), 1859–1863.CrossRef
Zurück zum Zitat Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., & Simmerling, C. (2006). Comparison of multiple AMBER force fields and development of improved protein backbone parameters. Proteins: Structure, Function, and Bioinformatics, 65, 712–725.CrossRef Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., & Simmerling, C. (2006). Comparison of multiple AMBER force fields and development of improved protein backbone parameters. Proteins: Structure, Function, and Bioinformatics, 65, 712–725.CrossRef
Zurück zum Zitat Hou, T., Wang, J., Li, Y., & Wang, W. (2011). Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. Journal of Chemical Information and Modeling, 51(1), 69–82.CrossRef Hou, T., Wang, J., Li, Y., & Wang, W. (2011). Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. Journal of Chemical Information and Modeling, 51(1), 69–82.CrossRef
Zurück zum Zitat Hsin, J., Arkhipov, A., Yin, Y., Stone, J. E., & Schulten, K. (2008). Using VMD: An introductory tutorial. Current Protocols in Bioinformatics, Chapter 5, Unit 5 7. Hsin, J., Arkhipov, A., Yin, Y., Stone, J. E., & Schulten, K. (2008). Using VMD: An introductory tutorial. Current Protocols in Bioinformatics, Chapter 5, Unit 5 7.
Zurück zum Zitat Huang, J., & MacKerell, A. D., Jr. (2013). CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data. Journal of Computational Chemistry, 34(25), 2135–2145.CrossRef Huang, J., & MacKerell, A. D., Jr. (2013). CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data. Journal of Computational Chemistry, 34(25), 2135–2145.CrossRef
Zurück zum Zitat Huang, J., Lopes, P. E., Roux, B., & MacKerell, A. D., Jr. (2014). Recent advances in polarizable force fields for macromolecules: Microsecond simulations of proteins using the classical drude oscillator model. Journal of Physical Chemistry Letters, 5(18), 3144–3150.CrossRef Huang, J., Lopes, P. E., Roux, B., & MacKerell, A. D., Jr. (2014). Recent advances in polarizable force fields for macromolecules: Microsecond simulations of proteins using the classical drude oscillator model. Journal of Physical Chemistry Letters, 5(18), 3144–3150.CrossRef
Zurück zum Zitat Huang, W., Manglik, A., Venkatakrishnan, A. J., Laeremans, T., Feinberg, E. N., Sanborn, A. L., et al. (2015). Structural insights into micro-opioid receptor activation. Nature, 524(7565),315–321.CrossRef Huang, W., Manglik, A., Venkatakrishnan, A. J., Laeremans, T., Feinberg, E. N., Sanborn, A. L., et al. (2015). Structural insights into micro-opioid receptor activation. Nature, 524(7565),315–321.CrossRef
Zurück zum Zitat Hub, J. S., & de Groot, B. L. (2009). Detection of functional modes in protein dynamics. PLoS Computational Biology, 5(8), e1000480.CrossRef Hub, J. S., & de Groot, B. L. (2009). Detection of functional modes in protein dynamics. PLoS Computational Biology, 5(8), e1000480.CrossRef
Zurück zum Zitat Hub, J. S., Grubmuller, H., & de Groot, B. L. (2009). Dynamics and energetics of permeation through aquaporins. What do we learn from molecular dynamics simulations? Handbook of Experimental Pharmacology, 190, 57–76.CrossRef Hub, J. S., Grubmuller, H., & de Groot, B. L. (2009). Dynamics and energetics of permeation through aquaporins. What do we learn from molecular dynamics simulations? Handbook of Experimental Pharmacology, 190, 57–76.CrossRef
Zurück zum Zitat Hummer, G., & Szabo, A. (2010). Free energy profiles from single-molecule pulling experiments. Proceedings of the National Academy of Sciences of the United States of America, 107(50), 21441–21446.CrossRef Hummer, G., & Szabo, A. (2010). Free energy profiles from single-molecule pulling experiments. Proceedings of the National Academy of Sciences of the United States of America, 107(50), 21441–21446.CrossRef
Zurück zum Zitat Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38, 27–38.CrossRef Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38, 27–38.CrossRef
Zurück zum Zitat Ikeguchi, M. (2009). Water transport in aquaporins: Molecular dynamics simulations. Frontiers in Bioscience, 14, 1283–1291.CrossRef Ikeguchi, M. (2009). Water transport in aquaporins: Molecular dynamics simulations. Frontiers in Bioscience, 14, 1283–1291.CrossRef
Zurück zum Zitat Ingolfsson, H. I., Lopez, C. A., Uusitalo, J. J., de Jong, D. H., Gopal, S. M., Periole, X., et al. (2014). The power of coarse graining in biomolecular simulations. Wiley Interdisciplinary Reviews: Computational Molecular Science, 4(3), 225–248. Ingolfsson, H. I., Lopez, C. A., Uusitalo, J. J., de Jong, D. H., Gopal, S. M., Periole, X., et al. (2014). The power of coarse graining in biomolecular simulations. Wiley Interdisciplinary Reviews: Computational Molecular Science, 4(3), 225–248.
Zurück zum Zitat Isaksen, G. V., Andberg, T. A. H., Åqvist, J., & Brandsdal, B. O. (2015). Qgui: A high-throughput interface for automated setup and analysis of free energy calculations and empirical valence bond simulations in biological systems. Journal of Molecular Graphics and Modelling, 60,15–23.CrossRef Isaksen, G. V., Andberg, T. A. H., Åqvist, J., & Brandsdal, B. O. (2015). Qgui: A high-throughput interface for automated setup and analysis of free energy calculations and empirical valence bond simulations in biological systems. Journal of Molecular Graphics and Modelling, 60,15–23.CrossRef
Zurück zum Zitat Ishida, H. (2014). Essential function of the N-termini tails of the proteasome for the gating mechanism revealed by molecular dynamics simulations. Proteins, 82(9), 1985–1999.CrossRef Ishida, H. (2014). Essential function of the N-termini tails of the proteasome for the gating mechanism revealed by molecular dynamics simulations. Proteins, 82(9), 1985–1999.CrossRef
Zurück zum Zitat Ito, Y., & Ikeguchi, M. (2014). Molecular dynamics simulations of F1-ATPase. In Protein conformational dynamics (pp. 411–440). Cham: Springer.CrossRef Ito, Y., & Ikeguchi, M. (2014). Molecular dynamics simulations of F1-ATPase. In Protein conformational dynamics (pp. 411–440). Cham: Springer.CrossRef
Zurück zum Zitat Iwasa, J. H. (2015). Bringing macromolecular machinery to life using 3D animation. Current Opinion in Structural Biology, 31, 84–88.CrossRef Iwasa, J. H. (2015). Bringing macromolecular machinery to life using 3D animation. Current Opinion in Structural Biology, 31, 84–88.CrossRef
Zurück zum Zitat Jankowski, M., Wertheim-Tysarowska, K., Jakubowski, R., Sota, J., Nowak, W., & Czajkowski, R. (2014). Novel KRT14 mutation causing epidermolysis bullosa simplex with variable phenotype. Experimental Dermatology, 23(9), 684–687.CrossRef Jankowski, M., Wertheim-Tysarowska, K., Jakubowski, R., Sota, J., Nowak, W., & Czajkowski, R. (2014). Novel KRT14 mutation causing epidermolysis bullosa simplex with variable phenotype. Experimental Dermatology, 23(9), 684–687.CrossRef
Zurück zum Zitat Jorgensen, W. L. (2013). Foundations of biomolecular modeling. Cell, 155(6), 1199–1202.CrossRef Jorgensen, W. L. (2013). Foundations of biomolecular modeling. Cell, 155(6), 1199–1202.CrossRef
Zurück zum Zitat Jorgensen, W. L., & Tirado-Rives, J. (1988). The Opls potential functions for proteins – Energy minimizations for crystals of cyclic-peptides and crambin. Journal of the American Chemical Society, 110(6), 1657–1666.CrossRef Jorgensen, W. L., & Tirado-Rives, J. (1988). The Opls potential functions for proteins – Energy minimizations for crystals of cyclic-peptides and crambin. Journal of the American Chemical Society, 110(6), 1657–1666.CrossRef
Zurück zum Zitat Kannan, S., & Zacharias, M. (2009). Simulated annealing coupled replica exchange molecular dynamics – An efficient conformational sampling method. Journal of Structural Biology, 166(3), 288–294.CrossRef Kannan, S., & Zacharias, M. (2009). Simulated annealing coupled replica exchange molecular dynamics – An efficient conformational sampling method. Journal of Structural Biology, 166(3), 288–294.CrossRef
Zurück zum Zitat Kardos, J., & Héja, L. (2015). How membrane proteins work giving autonomous traverse pathways? Structural Chemistry, 26(5–6), 1405–1410.CrossRef Kardos, J., & Héja, L. (2015). How membrane proteins work giving autonomous traverse pathways? Structural Chemistry, 26(5–6), 1405–1410.CrossRef
Zurück zum Zitat Karplus, M. (2003). Molecular dynamics of biological macromolecules: A brief history and perspective. Biopolymers, 68(3), 350–358.CrossRef Karplus, M. (2003). Molecular dynamics of biological macromolecules: A brief history and perspective. Biopolymers, 68(3), 350–358.CrossRef
Zurück zum Zitat Karplus, M. (2014). Development of multiscale models for complex chemical systems: From H + H(2) to biomolecules (Nobel lecture). Angewandte Chemie International Edition in English, 53(38), 9992–10005.CrossRef Karplus, M. (2014). Development of multiscale models for complex chemical systems: From H + H(2) to biomolecules (Nobel lecture). Angewandte Chemie International Edition in English, 53(38), 9992–10005.CrossRef
Zurück zum Zitat Karplus, M., & McCammon, J. A. (2002). Molecular dynamics simulations of biomolecules. Nature Structural Biology, 9(9), 646–652.CrossRef Karplus, M., & McCammon, J. A. (2002). Molecular dynamics simulations of biomolecules. Nature Structural Biology, 9(9), 646–652.CrossRef
Zurück zum Zitat Kassler, K., Horn, A. H. C., & Sticht, H. (2010). Effect of pathogenic mutations on the structure and dynamics of Alzheimer’s A beta(42)-amyloid oligomers. Journal of Molecular Modeling, 16(5), 1011–1020.CrossRef Kassler, K., Horn, A. H. C., & Sticht, H. (2010). Effect of pathogenic mutations on the structure and dynamics of Alzheimer’s A beta(42)-amyloid oligomers. Journal of Molecular Modeling, 16(5), 1011–1020.CrossRef
Zurück zum Zitat Khafizov, K., Lattanzi, G., & Carloni, P. (2009). G protein inactive and active forms investigated by simulation methods. Proteins: Structure, Function, and Bioinformatics, 75(4), 919–930.CrossRef Khafizov, K., Lattanzi, G., & Carloni, P. (2009). G protein inactive and active forms investigated by simulation methods. Proteins: Structure, Function, and Bioinformatics, 75(4), 919–930.CrossRef
Zurück zum Zitat Khalili-Araghi, F., Gumbart, J., Wen, P. C., Sotomayor, M., Tajkhorshid, E., & Schulten, K. (2009). Molecular dynamics simulations of membrane channels and transporters. Current Opinion in Structural Biology, 19(2), 128–137.CrossRef Khalili-Araghi, F., Gumbart, J., Wen, P. C., Sotomayor, M., Tajkhorshid, E., & Schulten, K. (2009). Molecular dynamics simulations of membrane channels and transporters. Current Opinion in Structural Biology, 19(2), 128–137.CrossRef
Zurück zum Zitat Kholmurodov, K. T., Altaisky, M. V., Puzynin, I. V., Darden, T., & Filatov, F. P. (2003). Methods of molecular dynamics for simulation of physical and biological processes. Physics of Particles and Nuclei, 34(2), 244–263. Kholmurodov, K. T., Altaisky, M. V., Puzynin, I. V., Darden, T., & Filatov, F. P. (2003). Methods of molecular dynamics for simulation of physical and biological processes. Physics of Particles and Nuclei, 34(2), 244–263.
Zurück zum Zitat Khurana, E., Devane, R. H., Dal Peraro, M., & Klein, M. L. (2011). Computational study of drug binding to the membrane-bound tetrameric M2 peptide bundle from influenza A virus. Biochimica et Biophysica Acta, 1808(2), 530–537.CrossRef Khurana, E., Devane, R. H., Dal Peraro, M., & Klein, M. L. (2011). Computational study of drug binding to the membrane-bound tetrameric M2 peptide bundle from influenza A virus. Biochimica et Biophysica Acta, 1808(2), 530–537.CrossRef
Zurück zum Zitat Kim, I., & Warshel, A. (2014). Coarse-grained simulations of the gating current in the voltage-activated Kv1.2 channel. Proceedings of the National Academy of Sciences of the United States of America, 111(6), 2128–2133.CrossRef Kim, I., & Warshel, A. (2014). Coarse-grained simulations of the gating current in the voltage-activated Kv1.2 channel. Proceedings of the National Academy of Sciences of the United States of America, 111(6), 2128–2133.CrossRef
Zurück zum Zitat Kingsley, L. J., & Lill, M. A. (2015). Substrate tunnels in enzymes: Structure-function relationships and computational methodology. Proteins, 83(4), 599–611.CrossRef Kingsley, L. J., & Lill, M. A. (2015). Substrate tunnels in enzymes: Structure-function relationships and computational methodology. Proteins, 83(4), 599–611.CrossRef
Zurück zum Zitat Klein, M. L., & Shinoda, W. (2008). Large-scale molecular dynamics simulations of self-assembling systems. Science, 321, 798–800.CrossRef Klein, M. L., & Shinoda, W. (2008). Large-scale molecular dynamics simulations of self-assembling systems. Science, 321, 798–800.CrossRef
Zurück zum Zitat Klepeis, J. L., Pieja, M. J., & Floudas, C. A. (2003). Hybrid global optimization algorithms for protein structure prediction: Alternating hybrids. Biophysical Journal, 84(2 Pt 1), 869–882.CrossRef Klepeis, J. L., Pieja, M. J., & Floudas, C. A. (2003). Hybrid global optimization algorithms for protein structure prediction: Alternating hybrids. Biophysical Journal, 84(2 Pt 1), 869–882.CrossRef
Zurück zum Zitat Klepeis, J. L., Lindorff-Larsen, K., Dror, R. O., & Shaw, D. E. (2009). Long-timescale molecular dynamics simulations of protein structure and function. Current Opinion in Structural Biology, 19(2), 120–127.CrossRef Klepeis, J. L., Lindorff-Larsen, K., Dror, R. O., & Shaw, D. E. (2009). Long-timescale molecular dynamics simulations of protein structure and function. Current Opinion in Structural Biology, 19(2), 120–127.CrossRef
Zurück zum Zitat Klimovich, P. V., Shirts, M. R., & Mobley, D. L. (2015). Guidelines for the analysis of free energy calculations. Journal of Computer-Aided Molecular Design, 29(5), 397–411.CrossRef Klimovich, P. V., Shirts, M. R., & Mobley, D. L. (2015). Guidelines for the analysis of free energy calculations. Journal of Computer-Aided Molecular Design, 29(5), 397–411.CrossRef
Zurück zum Zitat Kmiecik, S., Gront, D., & Kolinski, A. (2007). Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field. BMC Structural Biology, 7, 43.CrossRef Kmiecik, S., Gront, D., & Kolinski, A. (2007). Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field. BMC Structural Biology, 7, 43.CrossRef
Zurück zum Zitat Kmiecik, S., Wabik, J., Kolinski, M., Kouza, M., & Kolinski, A. (2014). Coarse-grained modeling of protein dynamics. In Computational methods to study the structure and dynamics of biomolecules and biomolecular processes (pp. 55–79). Berlin/Heidelberg: Springer.CrossRef Kmiecik, S., Wabik, J., Kolinski, M., Kouza, M., & Kolinski, A. (2014). Coarse-grained modeling of protein dynamics. In Computational methods to study the structure and dynamics of biomolecules and biomolecular processes (pp. 55–79). Berlin/Heidelberg: Springer.CrossRef
Zurück zum Zitat Knapp, B., & Schreiner, W. (2009). Graphical user interfaces for molecular dynamics-quo vadis? Bioinformatics and Biology Insights, 3, 103–107. Knapp, B., & Schreiner, W. (2009). Graphical user interfaces for molecular dynamics-quo vadis? Bioinformatics and Biology Insights, 3, 103–107.
Zurück zum Zitat Kohen, A. (2015). Dihydrofolate reductase as a model for studies of enzyme dynamics and catalysis [version 1; referees: 2 approved]. F1000Research, 4(F1000 Faculty Rev), 1464. doi:10.12688/f1000research.6968.1. Kohen, A. (2015). Dihydrofolate reductase as a model for studies of enzyme dynamics and catalysis [version 1; referees: 2 approved]. F1000Research, 4(F1000 Faculty Rev), 1464. doi:10.12688/f1000research.6968.1.
Zurück zum Zitat Kremer, K. (2003). Computer simulations for macromolecular science. Macromolecular Chemistry and Physics, 204(2), 257–264.CrossRef Kremer, K. (2003). Computer simulations for macromolecular science. Macromolecular Chemistry and Physics, 204(2), 257–264.CrossRef
Zurück zum Zitat Krieger, E., & Vriend, G. (2015). New ways to boost molecular dynamics simulations. Journal of Computational Chemistry, 36(13), 996–1007.CrossRef Krieger, E., & Vriend, G. (2015). New ways to boost molecular dynamics simulations. Journal of Computational Chemistry, 36(13), 996–1007.CrossRef
Zurück zum Zitat Kryshtafovych, A., Monastyrskyy, B., & Fidelis, K. (2016). CASP11 statistics and the prediction center evaluation system. Proteins: Structure, Function, and Bioinformatics. doi:10.1002/prot.25005. Kryshtafovych, A., Monastyrskyy, B., & Fidelis, K. (2016). CASP11 statistics and the prediction center evaluation system. Proteins: Structure, Function, and Bioinformatics. doi:10.1002/prot.25005.
Zurück zum Zitat Kubiak, K., & Nowak, W. (2008). Molecular dynamics simulations of the photoactive protein nitrile hydratase. Biophysical Journal, 94(10), 3824–3838.CrossRef Kubiak, K., & Nowak, W. (2008). Molecular dynamics simulations of the photoactive protein nitrile hydratase. Biophysical Journal, 94(10), 3824–3838.CrossRef
Zurück zum Zitat Kuczera, K., Jas, G. S., & Elber, R. (2009). Kinetics of helix unfolding: Molecular dynamics simulations with milestoning. The Journal of Physical Chemistry. A, 113(26), 7461–7473.CrossRef Kuczera, K., Jas, G. S., & Elber, R. (2009). Kinetics of helix unfolding: Molecular dynamics simulations with milestoning. The Journal of Physical Chemistry. A, 113(26), 7461–7473.CrossRef
Zurück zum Zitat Kukic, P., Kannan, A., Dijkstra, M. J., Abeln, S., Camilloni, C., & Vendruscolo, M. (2015). Mapping the protein fold universe using the CamTube force field in molecular dynamics simulations. PLoS Computational Biology, 11(10), e1004435.CrossRef Kukic, P., Kannan, A., Dijkstra, M. J., Abeln, S., Camilloni, C., & Vendruscolo, M. (2015). Mapping the protein fold universe using the CamTube force field in molecular dynamics simulations. PLoS Computational Biology, 11(10), e1004435.CrossRef
Zurück zum Zitat Kumar, S., & Li, M. S. (2010). Biomolecules under mechanical force. Physics Reports, 486(1–2), 1–74.CrossRef Kumar, S., & Li, M. S. (2010). Biomolecules under mechanical force. Physics Reports, 486(1–2), 1–74.CrossRef
Zurück zum Zitat Kumar, A., & Purohit, R. (2014). Use of long term molecular dynamics simulation in predicting cancer associated SNPs. PLoS Computational Biology, 10(4), e1003318.CrossRef Kumar, A., & Purohit, R. (2014). Use of long term molecular dynamics simulation in predicting cancer associated SNPs. PLoS Computational Biology, 10(4), e1003318.CrossRef
Zurück zum Zitat Kupfer, L., Hinrichs, W., & Groschup, M. H. (2009). Prion protein misfolding. Current Molecular Medicine, 9(7), 826–835.CrossRef Kupfer, L., Hinrichs, W., & Groschup, M. H. (2009). Prion protein misfolding. Current Molecular Medicine, 9(7), 826–835.CrossRef
Zurück zum Zitat Kutzner, C., Czub, J., & Grubmuller, H. (2011). Keep it flexible: Driving macromolecular rotary motions in atomistic simulations with GROMACS. Journal of Chemical Theory and Computation, 7(5), 1381–1393.CrossRef Kutzner, C., Czub, J., & Grubmuller, H. (2011). Keep it flexible: Driving macromolecular rotary motions in atomistic simulations with GROMACS. Journal of Chemical Theory and Computation, 7(5), 1381–1393.CrossRef
Zurück zum Zitat Lane, T. J., Shukla, D., Beauchamp, K. A., & Pande, V. S. (2013). To milliseconds and beyond: Challenges in the simulation of protein folding. Current Opinion in Structural Biology, 23(1), 58–65.CrossRef Lane, T. J., Shukla, D., Beauchamp, K. A., & Pande, V. S. (2013). To milliseconds and beyond: Challenges in the simulation of protein folding. Current Opinion in Structural Biology, 23(1), 58–65.CrossRef
Zurück zum Zitat Lange, O. E., Schafer, L. V., & Grubmuller, H. (2006). Flooding in GROMACS: Accelerated barrier crossings in molecular dynamics. Journal of Computational Chemistry, 27(14), 1693–1702.CrossRef Lange, O. E., Schafer, L. V., & Grubmuller, H. (2006). Flooding in GROMACS: Accelerated barrier crossings in molecular dynamics. Journal of Computational Chemistry, 27(14), 1693–1702.CrossRef
Zurück zum Zitat Lauria, A., Tutone, M., Ippolito, M., Pantano, L., & Almerico, A. M. (2010). Molecular modeling approaches in the discovery of new drugs for anti-cancer therapy: The investigation of p53-MDM2 interaction and its inhibition by small molecules. Current Medicinal Chemistry, 17(28), 3142–3154.CrossRef Lauria, A., Tutone, M., Ippolito, M., Pantano, L., & Almerico, A. M. (2010). Molecular modeling approaches in the discovery of new drugs for anti-cancer therapy: The investigation of p53-MDM2 interaction and its inhibition by small molecules. Current Medicinal Chemistry, 17(28), 3142–3154.CrossRef
Zurück zum Zitat Le, L., Lee, E., Schulten, K., & Truong, T. N. (2011). Molecular modeling of swine influenza A/H1N1, Spanish H1N1, and avian H5N1 flu N1 neuraminidases bound to Tamiflu and Relenza. PLoS Currents, 1, RRN1015. doi:10.1371/currents.RRN1015. Le, L., Lee, E., Schulten, K., & Truong, T. N. (2011). Molecular modeling of swine influenza A/H1N1, Spanish H1N1, and avian H5N1 flu N1 neuraminidases bound to Tamiflu and Relenza. PLoS Currents, 1, RRN1015. doi:10.1371/currents.RRN1015.
Zurück zum Zitat Leach, A. (2001). Molecular modelling: Principles and applications (2nd ed.). Harlow: Prentice Hall. Leach, A. (2001). Molecular modelling: Principles and applications (2nd ed.). Harlow: Prentice Hall.
Zurück zum Zitat Lee, G., Nowak, W., Jaroniec, J., Zhang, Q., & Marszalek, P. E. (2004). Nanomechanical control of glucopyranose rotamers. Journal of the American Chemical Society, 126(20), 6218–6219.CrossRef Lee, G., Nowak, W., Jaroniec, J., Zhang, Q., & Marszalek, P. E. (2004). Nanomechanical control of glucopyranose rotamers. Journal of the American Chemical Society, 126(20), 6218–6219.CrossRef
Zurück zum Zitat Lee, E. H., Hsin, J., Sotomayor, M., Comellas, G., & Schulten, K. (2009). Discovery through the computational microscope. Structure, 17(10), 1295–1306.CrossRef Lee, E. H., Hsin, J., Sotomayor, M., Comellas, G., & Schulten, K. (2009). Discovery through the computational microscope. Structure, 17(10), 1295–1306.CrossRef
Zurück zum Zitat Lee, J., Kim, J.-S., & Seok, C. (2010). Cooperativity and specificity of Cys2His2 Zinc finger protein – DNA interactions: A molecular dynamics simulation study. The Journal of Physical Chemistry B, 114(22), 7662–7671.CrossRef Lee, J., Kim, J.-S., & Seok, C. (2010). Cooperativity and specificity of Cys2His2 Zinc finger protein – DNA interactions: A molecular dynamics simulation study. The Journal of Physical Chemistry B, 114(22), 7662–7671.CrossRef
Zurück zum Zitat Lee, K. H., Kuczera, K., & Banaszak Holl, M. M. (2011). The severity of osteogenesis imperfecta: A comparison to the relative free energy differences of collagen model peptides. Biopolymers, 95(3), 182–193.CrossRef Lee, K. H., Kuczera, K., & Banaszak Holl, M. M. (2011). The severity of osteogenesis imperfecta: A comparison to the relative free energy differences of collagen model peptides. Biopolymers, 95(3), 182–193.CrossRef
Zurück zum Zitat Leszczynski, J. (2012). Handbook of computational chemistry. Dordrecht/New York: Springer.CrossRef Leszczynski, J. (2012). Handbook of computational chemistry. Dordrecht/New York: Springer.CrossRef
Zurück zum Zitat Levitt, M. (2014). Birth and future of multiscale modeling for macromolecular systems (Nobel lecture). Angewandte Chemie International Edition in English, 53(38), 10006–10018.CrossRef Levitt, M. (2014). Birth and future of multiscale modeling for macromolecular systems (Nobel lecture). Angewandte Chemie International Edition in English, 53(38), 10006–10018.CrossRef
Zurück zum Zitat Levitt, M., & Lifson, S. (1969). Refinement of protein conformation using a macromolecular energy minimization procedure. Journal of Molecular Biology, 46, 269–279.CrossRef Levitt, M., & Lifson, S. (1969). Refinement of protein conformation using a macromolecular energy minimization procedure. Journal of Molecular Biology, 46, 269–279.CrossRef
Zurück zum Zitat Li, Y., & Gong, H. (2015). Theoretical and simulation studies on voltage-gated sodium channels. Protein & Cell, 6(6), 413–422.CrossRef Li, Y., & Gong, H. (2015). Theoretical and simulation studies on voltage-gated sodium channels. Protein & Cell, 6(6), 413–422.CrossRef
Zurück zum Zitat Li, Q., Wanderling, S., Paduch, M., Medovoy, D., Singharoy, A., McGreevy, R., et al. (2014). Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain. Nature Structural & Molecular Biology, 21(3), 244–252.CrossRef Li, Q., Wanderling, S., Paduch, M., Medovoy, D., Singharoy, A., McGreevy, R., et al. (2014). Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain. Nature Structural & Molecular Biology, 21(3), 244–252.CrossRef
Zurück zum Zitat Linder, T., Wang, S., Zangerl-Plessl, E.-M., Nichols, C. G., & Stary-Weinzinger, A. (2015). Molecular dynamics simulations of KirBac1.1 mutants reveal global gating changes of Kir channels. Journal of Chemical Information and Modeling, 55(4), 814–822.CrossRef Linder, T., Wang, S., Zangerl-Plessl, E.-M., Nichols, C. G., & Stary-Weinzinger, A. (2015). Molecular dynamics simulations of KirBac1.1 mutants reveal global gating changes of Kir channels. Journal of Chemical Information and Modeling, 55(4), 814–822.CrossRef
Zurück zum Zitat Lindorff-Larsen, K., Maragakis, P., Piana, S., Eastwood, M. P., Dror, R. O., & Shaw, D. E. (2012a). Systematic validation of protein force fields against experimental data. PLoS One, 7(2), e32131.CrossRef Lindorff-Larsen, K., Maragakis, P., Piana, S., Eastwood, M. P., Dror, R. O., & Shaw, D. E. (2012a). Systematic validation of protein force fields against experimental data. PLoS One, 7(2), e32131.CrossRef
Zurück zum Zitat Lindorff-Larsen, K., Trbovic, N., Maragakis, P., Piana, S., & Shaw, D. E. (2012b). Structure and dynamics of an unfolded protein examined by molecular dynamics simulation. Journal of the American Chemical Society, 134(8), 3787–3791.CrossRef Lindorff-Larsen, K., Trbovic, N., Maragakis, P., Piana, S., & Shaw, D. E. (2012b). Structure and dynamics of an unfolded protein examined by molecular dynamics simulation. Journal of the American Chemical Society, 134(8), 3787–3791.CrossRef
Zurück zum Zitat Liu, J., & Nussinov, R. (2010). Molecular dynamics reveal the essential role of linker motions in the function of cullin-RING E3 ligases. Journal of Molecular Biology, 396(5),1508–1523.CrossRef Liu, J., & Nussinov, R. (2010). Molecular dynamics reveal the essential role of linker motions in the function of cullin-RING E3 ligases. Journal of Molecular Biology, 396(5),1508–1523.CrossRef
Zurück zum Zitat Liwo, A., Czaplewski, C., Oldziej, S., & Scheraga, H. A. (2008). Computational techniques for efficient conformational sampling of proteins. Current Opinion in Structural Biology, 18(2), 134–139.CrossRef Liwo, A., Czaplewski, C., Oldziej, S., & Scheraga, H. A. (2008). Computational techniques for efficient conformational sampling of proteins. Current Opinion in Structural Biology, 18(2), 134–139.CrossRef
Zurück zum Zitat Lonsdale, R., Ranaghan, K. E., & Mulholland, A. J. (2010). Computational enzymology. Chemical Communications, 46(14), 2354–2372.CrossRef Lonsdale, R., Ranaghan, K. E., & Mulholland, A. J. (2010). Computational enzymology. Chemical Communications, 46(14), 2354–2372.CrossRef
Zurück zum Zitat Lopes, P. E., Guvench, O., & MacKerell, A. D., Jr. (2015). Current status of protein force fields for molecular dynamics simulations. Methods in Molecular Biology, 1215, 47–71.CrossRef Lopes, P. E., Guvench, O., & MacKerell, A. D., Jr. (2015). Current status of protein force fields for molecular dynamics simulations. Methods in Molecular Biology, 1215, 47–71.CrossRef
Zurück zum Zitat Lorenz, C., & Doltsinis, N. L. (2012). Molecular dynamics simulation: From “Ab Initio” to “Coarse Grained”. In J. Leszczynski (Ed.), Handbook of computational chemistry (pp. 195–238). Dordrecht: Springer.CrossRef Lorenz, C., & Doltsinis, N. L. (2012). Molecular dynamics simulation: From “Ab Initio” to “Coarse Grained”. In J. Leszczynski (Ed.), Handbook of computational chemistry (pp. 195–238). Dordrecht: Springer.CrossRef
Zurück zum Zitat Lu, Z., Nowak, W., Lee, G., Marszalek, P. E., & Yang, W. (2004). Elastic properties of single amylose chains in water: A quantum mechanical and AFM study. Journal of the American Chemical Society, 126(29), 9033–9041.CrossRef Lu, Z., Nowak, W., Lee, G., Marszalek, P. E., & Yang, W. (2004). Elastic properties of single amylose chains in water: A quantum mechanical and AFM study. Journal of the American Chemical Society, 126(29), 9033–9041.CrossRef
Zurück zum Zitat Ma, B., & Levine, A. J. (2007). Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elements. Nucleic Acids Research, 35(22), 7733–7747.CrossRef Ma, B., & Levine, A. J. (2007). Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elements. Nucleic Acids Research, 35(22), 7733–7747.CrossRef
Zurück zum Zitat Ma, W., & Schulten, K. (2015). Mechanism of substrate translocation by a ring-shaped ATPase motor at millisecond resolution. Journal of the American Chemical Society, 137(8), 3031–3040.CrossRef Ma, W., & Schulten, K. (2015). Mechanism of substrate translocation by a ring-shaped ATPase motor at millisecond resolution. Journal of the American Chemical Society, 137(8), 3031–3040.CrossRef
Zurück zum Zitat Ma, J., Flynn, T. C., Cui, Q., Leslie, A. G., Walker, J. E., & Karplus, M. (2002). A dynamic analysis of the rotation mechanism for conformational change in F(1)-ATPase. Structure, 10(7), 921–931.CrossRef Ma, J., Flynn, T. C., Cui, Q., Leslie, A. G., Walker, J. E., & Karplus, M. (2002). A dynamic analysis of the rotation mechanism for conformational change in F(1)-ATPase. Structure, 10(7), 921–931.CrossRef
Zurück zum Zitat Mac Kerell, A. D., Jr., & Nilsson, L. (2008). Molecular dynamics simulations of nucleic acid-protein complexes. Current Opinion in Structural Biology, 18(2), 194–199.CrossRef Mac Kerell, A. D., Jr., & Nilsson, L. (2008). Molecular dynamics simulations of nucleic acid-protein complexes. Current Opinion in Structural Biology, 18(2), 194–199.CrossRef
Zurück zum Zitat MacKerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., et al. (1998). All-atom empirical potential for molecular modeling and dynamics studies of proteins. Journal of Physical Chemistry B, 102(18), 3586–3616.CrossRef MacKerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., et al. (1998). All-atom empirical potential for molecular modeling and dynamics studies of proteins. Journal of Physical Chemistry B, 102(18), 3586–3616.CrossRef
Zurück zum Zitat Malde, A. K., Zuo, L., Breeze, M., Stroet, M., Poger, D., Nair, P. C., et al. (2011). An automated force field topology builder (ATB) and repository: Version 1.0. Journal of Chemical Theory and Computation, 7(12), 4026–4037.CrossRef Malde, A. K., Zuo, L., Breeze, M., Stroet, M., Poger, D., Nair, P. C., et al. (2011). An automated force field topology builder (ATB) and repository: Version 1.0. Journal of Chemical Theory and Computation, 7(12), 4026–4037.CrossRef
Zurück zum Zitat Marrink, S. J., & Tieleman, D. P. (2013). Perspective on the Martini model. Chemical Society Reviews, 42(16), 6801–6822.CrossRef Marrink, S. J., & Tieleman, D. P. (2013). Perspective on the Martini model. Chemical Society Reviews, 42(16), 6801–6822.CrossRef
Zurück zum Zitat Martin, L., Bilek, M. M., Weiss, A. S., & Kuyucak, S. (2015). Force fields for simulating the interaction of surfaces with biological molecules. Interface Focus, 6(1). 10.1098/rsfs.2015.0045. Martin, L., Bilek, M. M., Weiss, A. S., & Kuyucak, S. (2015). Force fields for simulating the interaction of surfaces with biological molecules. Interface Focus, 6(1). 10.1098/rsfs.2015.0045.
Zurück zum Zitat Martin-Garcia, F., Papaleo, E., Gomez-Puertas, P., Boomsma, W., & Lindorff-Larsen, K. (2015). Comparing molecular dynamics force fields in the essential subspace. PLoS One, 10(3), e0121114.CrossRef Martin-Garcia, F., Papaleo, E., Gomez-Puertas, P., Boomsma, W., & Lindorff-Larsen, K. (2015). Comparing molecular dynamics force fields in the essential subspace. PLoS One, 10(3), e0121114.CrossRef
Zurück zum Zitat May, A., Pool, R., van Dijk, E., Bijlard, J., Abeln, S., Heringa, J., et al. (2014). Coarse-grained versus atomistic simulations: Realistic interaction free energies for real proteins. Bioinformatics, 30(3), 326–334.CrossRef May, A., Pool, R., van Dijk, E., Bijlard, J., Abeln, S., Heringa, J., et al. (2014). Coarse-grained versus atomistic simulations: Realistic interaction free energies for real proteins. Bioinformatics, 30(3), 326–334.CrossRef
Zurück zum Zitat Mayne, C. G., Saam, J., Schulten, K., Tajkhorshid, E., & Gumbart, J. C. (2013). Rapid parameterization of small molecules using the force field toolkit. Journal of Computational Chemistry, 34(32), 2757–2770.CrossRef Mayne, C. G., Saam, J., Schulten, K., Tajkhorshid, E., & Gumbart, J. C. (2013). Rapid parameterization of small molecules using the force field toolkit. Journal of Computational Chemistry, 34(32), 2757–2770.CrossRef
Zurück zum Zitat McCammon, J. A., Gelin, B. R., & Karplus, M. (1977). Dynamics of folded proteins. Nature, 267(5612), 585–590.CrossRef McCammon, J. A., Gelin, B. R., & Karplus, M. (1977). Dynamics of folded proteins. Nature, 267(5612), 585–590.CrossRef
Zurück zum Zitat McGreevy, R., Singharoy, A., Li, Q., Zhang, J., Xu, D., Perozo, E., et al. (2014). xMDFF: Molecular dynamics flexible fitting of low-resolution X-ray structures. Acta Crystallographica Section D: Biological Crystallography, 70(9), 2344–2355.CrossRef McGreevy, R., Singharoy, A., Li, Q., Zhang, J., Xu, D., Perozo, E., et al. (2014). xMDFF: Molecular dynamics flexible fitting of low-resolution X-ray structures. Acta Crystallographica Section D: Biological Crystallography, 70(9), 2344–2355.CrossRef
Zurück zum Zitat McGreevy, R., Teo, I., Singharoy, A., & Schulten, K. (2016). Advances in the molecular dynamics flexible fitting method for cryo-EM modeling. Methods, 100, 50–60. McGreevy, R., Teo, I., Singharoy, A., & Schulten, K. (2016). Advances in the molecular dynamics flexible fitting method for cryo-EM modeling. Methods, 100, 50–60.
Zurück zum Zitat Meirovitch, H. (2007). Recent developments in methodologies for calculating the entropy and free energy of biological systems by computer simulation. Current Opinion in Structural Biology, 17(2), 181–186.CrossRef Meirovitch, H. (2007). Recent developments in methodologies for calculating the entropy and free energy of biological systems by computer simulation. Current Opinion in Structural Biology, 17(2), 181–186.CrossRef
Zurück zum Zitat Miao, L., & Schulten, K. (2009). Transport-related structures and processes of the nuclear pore complex studied through molecular dynamics. Structure, 17(3), 449–459.CrossRef Miao, L., & Schulten, K. (2009). Transport-related structures and processes of the nuclear pore complex studied through molecular dynamics. Structure, 17(3), 449–459.CrossRef
Zurück zum Zitat Miao, Y., Feher, V. A., & McCammon, J. A. (2015). Gaussian accelerated molecular dynamics: Unconstrained enhanced sampling and free energy calculation. Journal of Chemical Theory and Computation, 11(8), 3584–3595.CrossRef Miao, Y., Feher, V. A., & McCammon, J. A. (2015). Gaussian accelerated molecular dynamics: Unconstrained enhanced sampling and free energy calculation. Journal of Chemical Theory and Computation, 11(8), 3584–3595.CrossRef
Zurück zum Zitat Mikulska, K., Pepłowski, Ł., & Nowak, W. (2011). Nanomechanics of Ig-like domains of human contactin (BIG-2). Journal of Molecular Modeling, 17(9), 2313–2323.CrossRef Mikulska, K., Pepłowski, Ł., & Nowak, W. (2011). Nanomechanics of Ig-like domains of human contactin (BIG-2). Journal of Molecular Modeling, 17(9), 2313–2323.CrossRef
Zurück zum Zitat Mikulska, K., Strzelecki, J., Balter, A., & Nowak, W. (2012). Nanomechanical unfolding ofα-neurexin: A major component of the synaptic junction. Chemical Physics Letters, 521,134–137.CrossRef Mikulska, K., Strzelecki, J., Balter, A., & Nowak, W. (2012). Nanomechanical unfolding ofα-neurexin: A major component of the synaptic junction. Chemical Physics Letters, 521,134–137.CrossRef
Zurück zum Zitat Mikulska, K., Strzelecki, J., & Nowak, W. (2014). Nanomechanics of β-rich proteins related to neuronal disorders studied by AFM, all-atom and coarse-grained MD methods. Journal of Molecular Modeling, 20(3), 1–10.CrossRef Mikulska, K., Strzelecki, J., & Nowak, W. (2014). Nanomechanics of β-rich proteins related to neuronal disorders studied by AFM, all-atom and coarse-grained MD methods. Journal of Molecular Modeling, 20(3), 1–10.CrossRef
Zurück zum Zitat Miller, B. T., Singh, R. P., Klauda, J. B., Hodoscek, M., Brooks, B. R., & Woodcock, H. L. (2008). CHARMMing: A new, flexible web portal for CHARMM. Journal of Chemical Information and Modeling, 48, 1920–1929.CrossRef Miller, B. T., Singh, R. P., Klauda, J. B., Hodoscek, M., Brooks, B. R., & Woodcock, H. L. (2008). CHARMMing: A new, flexible web portal for CHARMM. Journal of Chemical Information and Modeling, 48, 1920–1929.CrossRef
Zurück zum Zitat Monroe, J. I., El-Nahal, W. G., & Shirts, M. R. (2014). Investigating the mutation resistance of nonnucleoside inhibitors of HIV-RT using multiple microsecond atomistic simulations. Proteins, 82(1), 130–144.CrossRef Monroe, J. I., El-Nahal, W. G., & Shirts, M. R. (2014). Investigating the mutation resistance of nonnucleoside inhibitors of HIV-RT using multiple microsecond atomistic simulations. Proteins, 82(1), 130–144.CrossRef
Zurück zum Zitat Moradi, M., & Tajkhorshid, E. (2014). Computational recipe for efficient description of large-scale conformational changes in biomolecular systems. Journal of Chemical Theory and Computation, 10(7), 2866–2880.CrossRef Moradi, M., & Tajkhorshid, E. (2014). Computational recipe for efficient description of large-scale conformational changes in biomolecular systems. Journal of Chemical Theory and Computation, 10(7), 2866–2880.CrossRef
Zurück zum Zitat Moraitakis, G., Purkiss, A. G., & Goodfellow, J. M. (2003). Simulated dynamics and biological molecules. Reports on Progress in Physics, 66, 483–406.CrossRef Moraitakis, G., Purkiss, A. G., & Goodfellow, J. M. (2003). Simulated dynamics and biological molecules. Reports on Progress in Physics, 66, 483–406.CrossRef
Zurück zum Zitat Mornon, J.-P., Hoffmann, B., Jonic, S., Lehn, P., & Callebaut, I. (2015). Full-open and closed CFTR channels, with lateral tunnels from the cytoplasm and an alternative position of the F508 region, as revealed by molecular dynamics. Cellular and Molecular Life Sciences, 72(7), 1377–1403.CrossRef Mornon, J.-P., Hoffmann, B., Jonic, S., Lehn, P., & Callebaut, I. (2015). Full-open and closed CFTR channels, with lateral tunnels from the cytoplasm and an alternative position of the F508 region, as revealed by molecular dynamics. Cellular and Molecular Life Sciences, 72(7), 1377–1403.CrossRef
Zurück zum Zitat Morra, G., Meli, M., & Colombo, G. (2008). Molecular dynamics simulations of proteins and peptides: From folding to drug design. Current Protein and Peptide Science, 9(2), 181–196.CrossRef Morra, G., Meli, M., & Colombo, G. (2008). Molecular dynamics simulations of proteins and peptides: From folding to drug design. Current Protein and Peptide Science, 9(2), 181–196.CrossRef
Zurück zum Zitat Mortier, J., Rakers, C., Bermudez, M., Murgueitio, M. S., Riniker, S., & Wolber, G. (2015). The impact of molecular dynamics on drug design: Applications for the characterization of ligand–macromolecule complexes. Drug Discovery Today, 20(6), 686–702.CrossRef Mortier, J., Rakers, C., Bermudez, M., Murgueitio, M. S., Riniker, S., & Wolber, G. (2015). The impact of molecular dynamics on drug design: Applications for the characterization of ligand–macromolecule complexes. Drug Discovery Today, 20(6), 686–702.CrossRef
Zurück zum Zitat Mukherjee, S., & Warshel, A. (2012). Realistic simulations of the coupling between the protomotive force and the mechanical rotation of the F0-ATPase. Proceedings of the National Academy of Sciences of the United States of America, 109(37), 14876–14881.CrossRef Mukherjee, S., & Warshel, A. (2012). Realistic simulations of the coupling between the protomotive force and the mechanical rotation of the F0-ATPase. Proceedings of the National Academy of Sciences of the United States of America, 109(37), 14876–14881.CrossRef
Zurück zum Zitat Mukherjee, S., & Warshel, A. (2015a). Bronsted slopes based on single-molecule imaging data help to unveil the chemically coupled rotation in F1-ATPase. Proceedings of the National Academy of Sciences of the United States of America, 112(46), 14121–14122.CrossRef Mukherjee, S., & Warshel, A. (2015a). Bronsted slopes based on single-molecule imaging data help to unveil the chemically coupled rotation in F1-ATPase. Proceedings of the National Academy of Sciences of the United States of America, 112(46), 14121–14122.CrossRef
Zurück zum Zitat Mukherjee, S., & Warshel, A. (2015b). Dissecting the role of the gamma-subunit in the rotary-chemical coupling and torque generation of F1-ATPase. Proceedings of the National Academy of Sciences of the United States of America, 112(9), 2746–2751.CrossRef Mukherjee, S., & Warshel, A. (2015b). Dissecting the role of the gamma-subunit in the rotary-chemical coupling and torque generation of F1-ATPase. Proceedings of the National Academy of Sciences of the United States of America, 112(9), 2746–2751.CrossRef
Zurück zum Zitat Nasica-Labouze, J., Nguyen, P. H., Sterpone, F., Berthoumieu, O., Buchete, N.-V., Coté, S., et al. (2015). Amyloid β protein and Alzheimer’s disease: When computer simulations complement experimental studies. Chemical Reviews, 115(9), 3518–3563.CrossRef Nasica-Labouze, J., Nguyen, P. H., Sterpone, F., Berthoumieu, O., Buchete, N.-V., Coté, S., et al. (2015). Amyloid β protein and Alzheimer’s disease: When computer simulations complement experimental studies. Chemical Reviews, 115(9), 3518–3563.CrossRef
Zurück zum Zitat Nguyen, H., Maier, J., Huang, H., Perrone, V., & Simmerling, C. (2014). Folding simulations for proteins with diverse topologies are accessible in days with a physics-based force field and implicit solvent. Journal of the American Chemical Society, 136(40), 13959–13962.CrossRef Nguyen, H., Maier, J., Huang, H., Perrone, V., & Simmerling, C. (2014). Folding simulations for proteins with diverse topologies are accessible in days with a physics-based force field and implicit solvent. Journal of the American Chemical Society, 136(40), 13959–13962.CrossRef
Zurück zum Zitat Nielsen, S. O., Bulo, R. E., Moore, P. B., & Ensing, B. (2010). Recent progress in adaptive multiscale molecular dynamics simulations of soft matter. Physical Chemistry Chemical Physics, 12(39), 12401–12414.CrossRef Nielsen, S. O., Bulo, R. E., Moore, P. B., & Ensing, B. (2010). Recent progress in adaptive multiscale molecular dynamics simulations of soft matter. Physical Chemistry Chemical Physics, 12(39), 12401–12414.CrossRef
Zurück zum Zitat Noel, J. K., & Whitford, P. C. (2014). How simulations reveal dynamics, disorder, and the energy landscapes of biomolecular function. Israel Journal of Chemistry, 54(8–9), 1093–1107.CrossRef Noel, J. K., & Whitford, P. C. (2014). How simulations reveal dynamics, disorder, and the energy landscapes of biomolecular function. Israel Journal of Chemistry, 54(8–9), 1093–1107.CrossRef
Zurück zum Zitat Nowak, W., & Marszalek, P. (2005). Molecular dynamics simulations of single molecule atomic force microscope experiments. Singapore: World Scientific.CrossRef Nowak, W., & Marszalek, P. (2005). Molecular dynamics simulations of single molecule atomic force microscope experiments. Singapore: World Scientific.CrossRef
Zurück zum Zitat Nowak, W., Czerminski, R., & Elber, R. (1991). Reaction path study of ligand diffusion in proteins: Application of the self penalty walk (SPW) method to calculate reaction coordinates for the motion of CO through leghemoglobin. Journal of the American Chemical Society, 113(15), 5627–5637.CrossRef Nowak, W., Czerminski, R., & Elber, R. (1991). Reaction path study of ligand diffusion in proteins: Application of the self penalty walk (SPW) method to calculate reaction coordinates for the motion of CO through leghemoglobin. Journal of the American Chemical Society, 113(15), 5627–5637.CrossRef
Zurück zum Zitat Oliveira, A. S., Damas, J. M., Baptista, A. M., & Soares, C. M. (2014). Exploring O2 diffusion inA-type cytochrome c oxidases: Molecular dynamics simulations uncover two alternative channels towards the binuclear site. PLoS Computational Biology, 10(12), e1004010.CrossRef Oliveira, A. S., Damas, J. M., Baptista, A. M., & Soares, C. M. (2014). Exploring O2 diffusion inA-type cytochrome c oxidases: Molecular dynamics simulations uncover two alternative channels towards the binuclear site. PLoS Computational Biology, 10(12), e1004010.CrossRef
Zurück zum Zitat Olsen, S., Lamothe, K., & Martinez, T. J. (2010). Protonic gating of excited-state twisting and charge localization in GFP chromophores: A mechanistic hypothesis for reversible photoswitching. Journal of the American Chemical Society, 132(4), 1192–1193.CrossRef Olsen, S., Lamothe, K., & Martinez, T. J. (2010). Protonic gating of excited-state twisting and charge localization in GFP chromophores: A mechanistic hypothesis for reversible photoswitching. Journal of the American Chemical Society, 132(4), 1192–1193.CrossRef
Zurück zum Zitat Orlowski, S., & Nowak, W. (2007). Locally enhanced sampling molecular dynamics study of the dioxygen transport in human cytoglobin. Journal of Molecular Modeling, 13(6–7), 715–723.CrossRef Orlowski, S., & Nowak, W. (2007). Locally enhanced sampling molecular dynamics study of the dioxygen transport in human cytoglobin. Journal of Molecular Modeling, 13(6–7), 715–723.CrossRef
Zurück zum Zitat Orlowski, S., & Nowak, W. (2008). Topology and thermodynamics of gaseous ligands diffusion paths in human neuroglobin. Biosystems, 94(3), 263–266.CrossRef Orlowski, S., & Nowak, W. (2008). Topology and thermodynamics of gaseous ligands diffusion paths in human neuroglobin. Biosystems, 94(3), 263–266.CrossRef
Zurück zum Zitat Orozco, M. (2014). A theoretical view of protein dynamics. Chemical Society Reviews, 43(14), 5051–5066.CrossRef Orozco, M. (2014). A theoretical view of protein dynamics. Chemical Society Reviews, 43(14), 5051–5066.CrossRef
Zurück zum Zitat Ortore, G., & Martinelli, A. (2012). Computational studies on transthyretin. Current Medicinal Chemistry, 19(15), 2380–2387.CrossRef Ortore, G., & Martinelli, A. (2012). Computational studies on transthyretin. Current Medicinal Chemistry, 19(15), 2380–2387.CrossRef
Zurück zum Zitat Paci, E. (2002). High pressure simulations of biomolecules. Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology, 1595(1–2), 185–200.CrossRef Paci, E. (2002). High pressure simulations of biomolecules. Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology, 1595(1–2), 185–200.CrossRef
Zurück zum Zitat Paci, E., Caflisch, A., Pluckthun, A., & Karplus, M. (2001). Forces and energetics of hapten-antibody dissociation: A biased molecular dynamics simulation study. Journal of Molecular Biology, 314(3), 589–605.CrossRef Paci, E., Caflisch, A., Pluckthun, A., & Karplus, M. (2001). Forces and energetics of hapten-antibody dissociation: A biased molecular dynamics simulation study. Journal of Molecular Biology, 314(3), 589–605.CrossRef
Zurück zum Zitat Pande, V. S., Baker, I., Chapman, J., Elmer, S. P., Khaliq, S., Larson, S. M., et al. (2003). Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing. Biopolymers, 68, 91–109.CrossRef Pande, V. S., Baker, I., Chapman, J., Elmer, S. P., Khaliq, S., Larson, S. M., et al. (2003). Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing. Biopolymers, 68, 91–109.CrossRef
Zurück zum Zitat Pantelopulos, G. A., Mukherjee, S., & Voelz, V. A. (2015). Microsecond simulations of mdm2 and its complex with p53 yield insight into force field accuracy and conformational dynamics. Proteins, 83(9), 1665–1676.CrossRef Pantelopulos, G. A., Mukherjee, S., & Voelz, V. A. (2015). Microsecond simulations of mdm2 and its complex with p53 yield insight into force field accuracy and conformational dynamics. Proteins, 83(9), 1665–1676.CrossRef
Zurück zum Zitat Papaleo, E. (2015). Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: Strength in unity. Frontiers in Molecular Biosciences, 2, 28.CrossRef Papaleo, E. (2015). Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: Strength in unity. Frontiers in Molecular Biosciences, 2, 28.CrossRef
Zurück zum Zitat Papaleo, E., & Invernizzi, G. (2011). Conformational diseases: Structural studies of aggregation of polyglutamine proteins. Current Computer-Aided Drug Design, 7(1), 23–43.CrossRef Papaleo, E., & Invernizzi, G. (2011). Conformational diseases: Structural studies of aggregation of polyglutamine proteins. Current Computer-Aided Drug Design, 7(1), 23–43.CrossRef
Zurück zum Zitat Peplowski, L., Kubiak, K., & Nowak, W. (2008). Mechanical aspects of nitrile hydratase enzymatic activity. Steered molecular dynamics simulations of Pseudonocardia thermophila JCM 3095. Chemical Physics Letters, 467(1–3), 144–149.CrossRef Peplowski, L., Kubiak, K., & Nowak, W. (2008). Mechanical aspects of nitrile hydratase enzymatic activity. Steered molecular dynamics simulations of Pseudonocardia thermophila JCM 3095. Chemical Physics Letters, 467(1–3), 144–149.CrossRef
Zurück zum Zitat Perez, A., MacCallum, J. L., & Dill, K. A. (2015). Accelerating molecular simulations of proteins using Bayesian inference on weak information. Proceedings of the National Academy of Sciences of the United States of America, 112(38), 11846–11851.CrossRef Perez, A., MacCallum, J. L., & Dill, K. A. (2015). Accelerating molecular simulations of proteins using Bayesian inference on weak information. Proceedings of the National Academy of Sciences of the United States of America, 112(38), 11846–11851.CrossRef
Zurück zum Zitat Perilla, J. R., Goh, B. C., Cassidy, C. K., Liu, B., Bernardi, R. C., Rudack, T., et al. (2015). Molecular dynamics simulations of large macromolecular complexes. Current Opinion in Structural Biology, 31, 64–74.CrossRef Perilla, J. R., Goh, B. C., Cassidy, C. K., Liu, B., Bernardi, R. C., Rudack, T., et al. (2015). Molecular dynamics simulations of large macromolecular complexes. Current Opinion in Structural Biology, 31, 64–74.CrossRef
Zurück zum Zitat Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., et al. (2005). Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26(16), 1781–1802.CrossRef Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., et al. (2005). Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26(16), 1781–1802.CrossRef
Zurück zum Zitat Piana, S., Sarkar, K., Lindorff-Larsen, K., Guo, M., Gruebele, M., & Shaw, D. E. (2011). Computational design and experimental testing of the fastest-folding beta-sheet protein. Journal of Molecular Biology, 405(1), 43–48.CrossRef Piana, S., Sarkar, K., Lindorff-Larsen, K., Guo, M., Gruebele, M., & Shaw, D. E. (2011). Computational design and experimental testing of the fastest-folding beta-sheet protein. Journal of Molecular Biology, 405(1), 43–48.CrossRef
Zurück zum Zitat Piana, S., Lindorff-Larsen, K., & Shaw, D. E. (2013). Atomic-level description of ubiquitin folding. Proceedings of the National Academy of Sciences of the United States of America, 110(15), 5915–5920.CrossRef Piana, S., Lindorff-Larsen, K., & Shaw, D. E. (2013). Atomic-level description of ubiquitin folding. Proceedings of the National Academy of Sciences of the United States of America, 110(15), 5915–5920.CrossRef
Zurück zum Zitat Piana, S., Klepeis, J. L., & Shaw, D. E. (2014). Assessing the accuracy of physical models used in protein-folding simulations: Quantitative evidence from long molecular dynamics simulations. Current Opinion in Structural Biology, 24, 98–105.CrossRef Piana, S., Klepeis, J. L., & Shaw, D. E. (2014). Assessing the accuracy of physical models used in protein-folding simulations: Quantitative evidence from long molecular dynamics simulations. Current Opinion in Structural Biology, 24, 98–105.CrossRef
Zurück zum Zitat Piana, S., Donchev, A. G., Robustelli, P., & Shaw, D. E. (2015). Water dispersion interactions strongly influence simulated structural properties of disordered protein States. Journal of Physical Chemistry B, 119(16), 5113–5123.CrossRef Piana, S., Donchev, A. G., Robustelli, P., & Shaw, D. E. (2015). Water dispersion interactions strongly influence simulated structural properties of disordered protein States. Journal of Physical Chemistry B, 119(16), 5113–5123.CrossRef
Zurück zum Zitat Piela, L. (2014). Chapter 1 – The magic of quantum mechanics. In Ideas of quantum chemistry (2nd ed., pp. 1–59). Oxford: Elsevier.CrossRef Piela, L. (2014). Chapter 1 – The magic of quantum mechanics. In Ideas of quantum chemistry (2nd ed., pp. 1–59). Oxford: Elsevier.CrossRef
Zurück zum Zitat Pohorille, A., Jarzynski, C., & Chipot, C. (2010). Good practices in free-energy calculations. Journal of Physical Chemistry B, 114(32), 10235–10253.CrossRef Pohorille, A., Jarzynski, C., & Chipot, C. (2010). Good practices in free-energy calculations. Journal of Physical Chemistry B, 114(32), 10235–10253.CrossRef
Zurück zum Zitat Pronk, S., Páll, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., et al. (2013). GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics, 29(7), 845–854.CrossRef Pronk, S., Páll, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., et al. (2013). GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics, 29(7), 845–854.CrossRef
Zurück zum Zitat Rahman, A., & Stillinger, F. H. (1971). Molecular dynamics study of liquid water. The Journal of Chemical Physics, 55, 3336–3359.CrossRef Rahman, A., & Stillinger, F. H. (1971). Molecular dynamics study of liquid water. The Journal of Chemical Physics, 55, 3336–3359.CrossRef
Zurück zum Zitat Rapaport, D. C. (1995). The art of molecular dynamics simulation. Cambridge, UK: Cambridge University Press. Rapaport, D. C. (1995). The art of molecular dynamics simulation. Cambridge, UK: Cambridge University Press.
Zurück zum Zitat Rauscher, S., Gapsys, V., Gajda, M. J., Zweckstetter, M., de Groot, B. L., & Grubmuller, H. (2015). Structural ensembles of intrinsically disordered proteins depend strongly on force field: A comparison to experiment. Journal of Chemical Theory and Computation, 11(11), 5513–5524.CrossRef Rauscher, S., Gapsys, V., Gajda, M. J., Zweckstetter, M., de Groot, B. L., & Grubmuller, H. (2015). Structural ensembles of intrinsically disordered proteins depend strongly on force field: A comparison to experiment. Journal of Chemical Theory and Computation, 11(11), 5513–5524.CrossRef
Zurück zum Zitat Reddy, T., & Sansom, M. S. (2016). Computational virology: From the inside out. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1858(7, Part B), 1610–1618. Reddy, T., & Sansom, M. S. (2016). Computational virology: From the inside out. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1858(7, Part B), 1610–1618.
Zurück zum Zitat Reddy, T., Shorthouse, D., Parton, D. L., Jefferys, E., Fowler, P. W., Chavent, M., et al. (2015). Nothing to sneeze at: A dynamic and integrative computational model of an influenza a virion. Structure, 23(3), 584–597.CrossRef Reddy, T., Shorthouse, D., Parton, D. L., Jefferys, E., Fowler, P. W., Chavent, M., et al. (2015). Nothing to sneeze at: A dynamic and integrative computational model of an influenza a virion. Structure, 23(3), 584–597.CrossRef
Zurück zum Zitat Rehm, S., Trodler, P., & Pleiss, J. (2010). Solvent-induced lid opening in lipases: A molecular dynamics study. Protein Science, 19(11), 2122–2130.CrossRef Rehm, S., Trodler, P., & Pleiss, J. (2010). Solvent-induced lid opening in lipases: A molecular dynamics study. Protein Science, 19(11), 2122–2130.CrossRef
Zurück zum Zitat Rico, F., Gonzalez, L., Casuso, I., Puig-Vidal, M., & Scheuring, S. (2013). High-speed force spectroscopy unfolds titin at the velocity of molecular dynamics simulations. Science, 342(6159), 741–743.CrossRef Rico, F., Gonzalez, L., Casuso, I., Puig-Vidal, M., & Scheuring, S. (2013). High-speed force spectroscopy unfolds titin at the velocity of molecular dynamics simulations. Science, 342(6159), 741–743.CrossRef
Zurück zum Zitat Rief, M., & Grubmuller, H. (2002). Force spectroscopy of single biomolecules. Chemphyschem, 3(3), 255–261.CrossRef Rief, M., & Grubmuller, H. (2002). Force spectroscopy of single biomolecules. Chemphyschem, 3(3), 255–261.CrossRef
Zurück zum Zitat Ritchie, D. W. (2008). Recent progress and future directions in protein-protein docking. Current Protein and Peptide Science, 9(1), 1–15.CrossRef Ritchie, D. W. (2008). Recent progress and future directions in protein-protein docking. Current Protein and Peptide Science, 9(1), 1–15.CrossRef
Zurück zum Zitat Rizzuti, B., & Daggett, V. (2013). Using simulations to provide the framework for experimental protein folding studies. Archives of Biochemistry and Biophysics, 531(1), 128–135.CrossRef Rizzuti, B., & Daggett, V. (2013). Using simulations to provide the framework for experimental protein folding studies. Archives of Biochemistry and Biophysics, 531(1), 128–135.CrossRef
Zurück zum Zitat Robustelli, P., Kohlhoff, K., Cavalli, A., & Vendruscolo, M. (2010). Using NMR chemical shifts as structural restraints in molecular dynamics simulations of proteins. Structure, 18(8), 923–933.CrossRef Robustelli, P., Kohlhoff, K., Cavalli, A., & Vendruscolo, M. (2010). Using NMR chemical shifts as structural restraints in molecular dynamics simulations of proteins. Structure, 18(8), 923–933.CrossRef
Zurück zum Zitat Rodrigues, J. R., Simoes, C. J. V., Silva, C. G., & Brito, R. M. M. (2010). Potentially amyloidogenic conformational intermediates populate the unfolding landscape of transthyretin: Insights from molecular dynamics simulations. Protein Science, 19(2), 202–219.CrossRef Rodrigues, J. R., Simoes, C. J. V., Silva, C. G., & Brito, R. M. M. (2010). Potentially amyloidogenic conformational intermediates populate the unfolding landscape of transthyretin: Insights from molecular dynamics simulations. Protein Science, 19(2), 202–219.CrossRef
Zurück zum Zitat Rohs, R., West, S. M., Liu, P., & Honig, B. (2009). Nuance in the double-helix and its role in protein–DNA recognition. Current Opinion in Structural Biology, 19(2), 171–177.CrossRef Rohs, R., West, S. M., Liu, P., & Honig, B. (2009). Nuance in the double-helix and its role in protein–DNA recognition. Current Opinion in Structural Biology, 19(2), 171–177.CrossRef
Zurück zum Zitat Romanowska, J., Setny, P., & Trylska, J. (2008). Molecular dynamics study of the ribosomal A-site. Journal of Physical Chemistry B, 112(47), 15227–15243.CrossRef Romanowska, J., Setny, P., & Trylska, J. (2008). Molecular dynamics study of the ribosomal A-site. Journal of Physical Chemistry B, 112(47), 15227–15243.CrossRef
Zurück zum Zitat Rosales-Hernandez, M. C., Bermudez-Lugo, J., Garcia, J., Trujillo-Ferrara, J., & Correa-Basurto, J. (2009). Molecular modeling applied to anti-cancer drug development. Anti-Cancer Agents in Medicinal Chemistry, 9(2), 230–238.CrossRef Rosales-Hernandez, M. C., Bermudez-Lugo, J., Garcia, J., Trujillo-Ferrara, J., & Correa-Basurto, J. (2009). Molecular modeling applied to anti-cancer drug development. Anti-Cancer Agents in Medicinal Chemistry, 9(2), 230–238.CrossRef
Zurück zum Zitat Rossle, S. C., & Frank, I. (2009). First-principles simulation of photoreactions in biological systems. Frontiers in Bioscience, 14, 4862–4877.CrossRef Rossle, S. C., & Frank, I. (2009). First-principles simulation of photoreactions in biological systems. Frontiers in Bioscience, 14, 4862–4877.CrossRef
Zurück zum Zitat Russel, D., Lasker, K., Phillips, J., Schneidman-Duhovny, D., Velazquez-Muriel, J. A., & Sali, A. (2009). The structural dynamics of macromolecular processes. Current Opinion in Cell Biology, 21(1), 97–108.CrossRef Russel, D., Lasker, K., Phillips, J., Schneidman-Duhovny, D., Velazquez-Muriel, J. A., & Sali, A. (2009). The structural dynamics of macromolecular processes. Current Opinion in Cell Biology, 21(1), 97–108.CrossRef
Zurück zum Zitat Rydzewski, J., & Nowak, W. (2015). Memetic algorithms for ligand expulsion from protein cavities. The Journal of Chemical Physics, 143(12), 124101.CrossRef Rydzewski, J., & Nowak, W. (2015). Memetic algorithms for ligand expulsion from protein cavities. The Journal of Chemical Physics, 143(12), 124101.CrossRef
Zurück zum Zitat Rydzewski, J., Jakubowski, R., & Nowak, W. (2015a). Communication: Entropic measure to prevent energy over-minimization in molecular dynamics simulations. The Journal of Chemical Physics, 143(17), 171103.CrossRef Rydzewski, J., Jakubowski, R., & Nowak, W. (2015a). Communication: Entropic measure to prevent energy over-minimization in molecular dynamics simulations. The Journal of Chemical Physics, 143(17), 171103.CrossRef
Zurück zum Zitat Rydzewski, J., Strzalka, W., & Nowak, W. (2015b). Nanomechanics of PCNA: A protein-made DNA sliding clamp. Chemical Physics Letters, 634, 236–242.CrossRef Rydzewski, J., Strzalka, W., & Nowak, W. (2015b). Nanomechanics of PCNA: A protein-made DNA sliding clamp. Chemical Physics Letters, 634, 236–242.CrossRef
Zurück zum Zitat Sagui, C., & Darden, T. A. (1999). Molecular dynamics simulations of biomolecules: Long-range electrostatic effects. Annual Review of Biophysics and Biomolecular Structure, 28(1), 155–179.CrossRef Sagui, C., & Darden, T. A. (1999). Molecular dynamics simulations of biomolecules: Long-range electrostatic effects. Annual Review of Biophysics and Biomolecular Structure, 28(1), 155–179.CrossRef
Zurück zum Zitat Sakudo, A., Xue, G. A., Kawashita, N., Ano, Y., Takagi, T., Shintani, H., et al. (2010). Structure of the prion protein and its gene: An analysis using bioinformatics and computer simulation. Current Protein & Peptide Science, 11(2), 166–179.CrossRef Sakudo, A., Xue, G. A., Kawashita, N., Ano, Y., Takagi, T., Shintani, H., et al. (2010). Structure of the prion protein and its gene: An analysis using bioinformatics and computer simulation. Current Protein & Peptide Science, 11(2), 166–179.CrossRef
Zurück zum Zitat Salmas, R. E., Yurtsever, M., & Durdagi, S. (2015). Investigation of inhibition mechanism of chemokine receptor CCR5 by micro-second molecular dynamics simulations. Scientific Reports, 5, 13180.CrossRef Salmas, R. E., Yurtsever, M., & Durdagi, S. (2015). Investigation of inhibition mechanism of chemokine receptor CCR5 by micro-second molecular dynamics simulations. Scientific Reports, 5, 13180.CrossRef
Zurück zum Zitat Salomon-Ferrer, R., Gotz, A. W., Poole, D., Le Grand, S., & Walker, R. C. (2013). Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. Explicit solvent particle Mesh Ewald. Journal of Chemical Theory and Computation, 9(9), 3878–3888.CrossRef Salomon-Ferrer, R., Gotz, A. W., Poole, D., Le Grand, S., & Walker, R. C. (2013). Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. Explicit solvent particle Mesh Ewald. Journal of Chemical Theory and Computation, 9(9), 3878–3888.CrossRef
Zurück zum Zitat Sanbonmatsu, K. Y. (2012). Computational studies of molecular machines: The ribosome. Current Opinion in Structural Biology, 22(2), 168–174.CrossRef Sanbonmatsu, K. Y. (2012). Computational studies of molecular machines: The ribosome. Current Opinion in Structural Biology, 22(2), 168–174.CrossRef
Zurück zum Zitat Sanbonmatsu, K. Y., & Tung, C. S. (2007). High performance computing in biology: Multimillion atom simulations of nanoscale systems. Journal of Structural Biology, 157(3), 470–480.CrossRef Sanbonmatsu, K. Y., & Tung, C. S. (2007). High performance computing in biology: Multimillion atom simulations of nanoscale systems. Journal of Structural Biology, 157(3), 470–480.CrossRef
Zurück zum Zitat Sansom, M. S., Scott, K. A., & Bond, P. J. (2008). Coarse-grained simulation: A high-throughput computational approach to membrane proteins. Biochemical Society Transactions, 36(Pt 1),27–32.CrossRef Sansom, M. S., Scott, K. A., & Bond, P. J. (2008). Coarse-grained simulation: A high-throughput computational approach to membrane proteins. Biochemical Society Transactions, 36(Pt 1),27–32.CrossRef
Zurück zum Zitat Saunders, M. G., & Voth, G. A. (2013). Coarse-graining methods for computational biology. Annual Review of Biophysics, 41(42), 73–93.CrossRef Saunders, M. G., & Voth, G. A. (2013). Coarse-graining methods for computational biology. Annual Review of Biophysics, 41(42), 73–93.CrossRef
Zurück zum Zitat Sborgi, L., Verma, A., Piana, S., Lindorff-Larsen, K., Cerminara, M., Santiveri, C. M., et al. (2015). Interaction networks in protein folding via atomic-resolution experiments and long-time-scale molecular dynamics simulations. Journal of the American Chemical Society, 137(20), 6506–6516.CrossRef Sborgi, L., Verma, A., Piana, S., Lindorff-Larsen, K., Cerminara, M., Santiveri, C. M., et al. (2015). Interaction networks in protein folding via atomic-resolution experiments and long-time-scale molecular dynamics simulations. Journal of the American Chemical Society, 137(20), 6506–6516.CrossRef
Zurück zum Zitat Scarpazza, D. P., Ierardi, D. J., Lerer, A. K., Mackenzie, K. M., Pan, A. C., Bank, J. A., et al. (2013). Extending the generality of molecular dynamics simulations on a special-purpose machine. In Ieee 27th international parallel and distributed processing symposium (Ipdps 2013), Boston, pp. 933–945. Scarpazza, D. P., Ierardi, D. J., Lerer, A. K., Mackenzie, K. M., Pan, A. C., Bank, J. A., et al. (2013). Extending the generality of molecular dynamics simulations on a special-purpose machine. In Ieee 27th international parallel and distributed processing symposium (Ipdps 2013), Boston, pp. 933–945.
Zurück zum Zitat Scheraga, H. A., Khalili, M., & Liwo, A. (2007). Protein-folding dynamics: Overview of molecular simulation techniques. Annual Review of Physical Chemistry, 58, 57–83.CrossRef Scheraga, H. A., Khalili, M., & Liwo, A. (2007). Protein-folding dynamics: Overview of molecular simulation techniques. Annual Review of Physical Chemistry, 58, 57–83.CrossRef
Zurück zum Zitat Scheres, S. H. (2010). Visualizing molecular machines in action: Single-particle analysis with structural variability. Advances in Protein Chemistry and Structural Biology, 81, 89–119.CrossRef Scheres, S. H. (2010). Visualizing molecular machines in action: Single-particle analysis with structural variability. Advances in Protein Chemistry and Structural Biology, 81, 89–119.CrossRef
Zurück zum Zitat Schlegel, H. B. (2003). Exploring potential energy surfaces for chemical reactions: An overview of some practical methods. Journal of Computational Chemistry, 24(12), 1514–1527.CrossRef Schlegel, H. B. (2003). Exploring potential energy surfaces for chemical reactions: An overview of some practical methods. Journal of Computational Chemistry, 24(12), 1514–1527.CrossRef
Zurück zum Zitat Schlick, T. (2010). Molecular modeling and simulation: An interdisciplinary guide: An interdisciplinary guide. New York: Springer.CrossRef Schlick, T. (2010). Molecular modeling and simulation: An interdisciplinary guide: An interdisciplinary guide. New York: Springer.CrossRef
Zurück zum Zitat Schuyler, A. D., Carlson, H. A., & Feldman, E. L. (2009). Computational methods for predicting sites of functionally important dynamics. Journal of Physical Chemistry B, 113(19), 6613–6622.CrossRef Schuyler, A. D., Carlson, H. A., & Feldman, E. L. (2009). Computational methods for predicting sites of functionally important dynamics. Journal of Physical Chemistry B, 113(19), 6613–6622.CrossRef
Zurück zum Zitat Schwede, T., & Peitsch, M. C. (2008). Computational structural biology: Methods and applications. Hackensack: World Scientific.CrossRef Schwede, T., & Peitsch, M. C. (2008). Computational structural biology: Methods and applications. Hackensack: World Scientific.CrossRef
Zurück zum Zitat Sen, S., Andreatta, D., Ponomarev, S. Y., Beveridge, D. L., & Berg, M. A. (2009). Dynamics of water and ions near DNA: Comparison of simulation to time-resolved stokes-shift experiments. Journal of the American Chemical Society, 131(5), 1724–1735.CrossRef Sen, S., Andreatta, D., Ponomarev, S. Y., Beveridge, D. L., & Berg, M. A. (2009). Dynamics of water and ions near DNA: Comparison of simulation to time-resolved stokes-shift experiments. Journal of the American Chemical Society, 131(5), 1724–1735.CrossRef
Zurück zum Zitat Shakhnovich, E. (2006). Protein folding thermodynamics and dynamics: Where physics, chemistry, and biology meet. Chemical Reviews, 106(5), 1559–1588.CrossRef Shakhnovich, E. (2006). Protein folding thermodynamics and dynamics: Where physics, chemistry, and biology meet. Chemical Reviews, 106(5), 1559–1588.CrossRef
Zurück zum Zitat Shaw, D. E., Grossman, J. P., Bank, J. A., Batson, B., Butts, J. A., Chao, J. C., et al. (2014). Anton 2: Raising the bar for performance and programmability in a special-purpose molecular dynamics supercomputer. In Paper presented at the proceedings of the international conference for high performance computing, networking, storage and analysis, New Orleans. Shaw, D. E., Grossman, J. P., Bank, J. A., Batson, B., Butts, J. A., Chao, J. C., et al. (2014). Anton 2: Raising the bar for performance and programmability in a special-purpose molecular dynamics supercomputer. In Paper presented at the proceedings of the international conference for high performance computing, networking, storage and analysis, New Orleans.
Zurück zum Zitat Sherwood, P., Brooks, B. R., & Sansom, M. S. (2008). Multiscale methods for macromolecular simulations. Current Opinion in Structural Biology, 18(5), 630–640.CrossRef Sherwood, P., Brooks, B. R., & Sansom, M. S. (2008). Multiscale methods for macromolecular simulations. Current Opinion in Structural Biology, 18(5), 630–640.CrossRef
Zurück zum Zitat Sieben, C., Kappel, C., Zhu, R., Wozniak, A., Rankl, C., Hinterdorfer, P., et al. (2012). Influenza virus binds its host cell using multiple dynamic interactions. Proceedings of the National Academy of Sciences of the United States of America, 109(34), 13626–13631.CrossRef Sieben, C., Kappel, C., Zhu, R., Wozniak, A., Rankl, C., Hinterdorfer, P., et al. (2012). Influenza virus binds its host cell using multiple dynamic interactions. Proceedings of the National Academy of Sciences of the United States of America, 109(34), 13626–13631.CrossRef
Zurück zum Zitat Sigg, D. (2014). Modeling ion channels: Past, present, and future. The Journal of General Physiology, 144(1), 7–26.CrossRef Sigg, D. (2014). Modeling ion channels: Past, present, and future. The Journal of General Physiology, 144(1), 7–26.CrossRef
Zurück zum Zitat Simonson, T., Archontis, G., & Karplus, M. (2002). Free energy simulations come of age: Protein-ligand recognition. Accounts of Chemical Research, 35(6), 430–437.CrossRef Simonson, T., Archontis, G., & Karplus, M. (2002). Free energy simulations come of age: Protein-ligand recognition. Accounts of Chemical Research, 35(6), 430–437.CrossRef
Zurück zum Zitat Sothiselvam, S., Liu, B., Han, W., Ramu, H., Klepacki, D., Atkinson, G. C., et al. (2014). Macrolide antibiotics allosterically predispose the ribosome for translation arrest. Proceedings of the National Academy of Sciences of the United States of America, 111(27), 9804–9809.CrossRef Sothiselvam, S., Liu, B., Han, W., Ramu, H., Klepacki, D., Atkinson, G. C., et al. (2014). Macrolide antibiotics allosterically predispose the ribosome for translation arrest. Proceedings of the National Academy of Sciences of the United States of America, 111(27), 9804–9809.CrossRef
Zurück zum Zitat Sotomayor, M., & Schulten, K. (2007). Single-molecule experiments in vitro and in silico. Science, 316(5828), 1144–1148.CrossRef Sotomayor, M., & Schulten, K. (2007). Single-molecule experiments in vitro and in silico. Science, 316(5828), 1144–1148.CrossRef
Zurück zum Zitat Spiwok, V., Sucur, Z., & Hosek, P. (2015). Enhanced sampling techniques in biomolecular simulations. Biotechnology Advances, 33(6 Pt 2), 1130–1140.CrossRef Spiwok, V., Sucur, Z., & Hosek, P. (2015). Enhanced sampling techniques in biomolecular simulations. Biotechnology Advances, 33(6 Pt 2), 1130–1140.CrossRef
Zurück zum Zitat Spyrakis, F., BidonChanal, A., Barril, X., & Luque, F. J. (2011). Protein flexibility and ligand recognition: Challenges for molecular modeling. Current Topics in Medicinal Chemistry, 11(2), 192–210.CrossRef Spyrakis, F., BidonChanal, A., Barril, X., & Luque, F. J. (2011). Protein flexibility and ligand recognition: Challenges for molecular modeling. Current Topics in Medicinal Chemistry, 11(2), 192–210.CrossRef
Zurück zum Zitat Stansfeld, P. J., & Sansom, M. S. (2011a). From coarse grained to atomistic: A serial multiscale approach to membrane protein simulations. Journal of Chemical Theory and Computation, 7(4), 1157–1166.CrossRef Stansfeld, P. J., & Sansom, M. S. (2011a). From coarse grained to atomistic: A serial multiscale approach to membrane protein simulations. Journal of Chemical Theory and Computation, 7(4), 1157–1166.CrossRef
Zurück zum Zitat Stansfeld, P. J., & Sansom, M. S. (2011b). Molecular simulation approaches to membrane proteins. Structure, 19(11), 1562–1572.CrossRef Stansfeld, P. J., & Sansom, M. S. (2011b). Molecular simulation approaches to membrane proteins. Structure, 19(11), 1562–1572.CrossRef
Zurück zum Zitat Stansfeld, P. J., Goose, J. E., Caffrey, M., Carpenter, E. P., Parker, J. L., Newstead, S., et al. (2015). MemProtMD: Automated insertion of membrane protein structures into explicit lipid membranes. Structure, 23(7), 1350–1361.CrossRef Stansfeld, P. J., Goose, J. E., Caffrey, M., Carpenter, E. P., Parker, J. L., Newstead, S., et al. (2015). MemProtMD: Automated insertion of membrane protein structures into explicit lipid membranes. Structure, 23(7), 1350–1361.CrossRef
Zurück zum Zitat Stone, J. E., Phillips, J. C., Freddolino, P. L., Hardy, D. J., Trabuco, L. G., & Schulten, K. (2007). Accelerating molecular modeling applications with graphics processors. Journal of Computational Chemistry, 28(16), 2618–2640.CrossRef Stone, J. E., Phillips, J. C., Freddolino, P. L., Hardy, D. J., Trabuco, L. G., & Schulten, K. (2007). Accelerating molecular modeling applications with graphics processors. Journal of Computational Chemistry, 28(16), 2618–2640.CrossRef
Zurück zum Zitat Straatsma, T. P., & McCammon, J. A. (1992). Computational alchemy. Annual Review of Physical Chemistry, 43, 407–435.CrossRef Straatsma, T. P., & McCammon, J. A. (1992). Computational alchemy. Annual Review of Physical Chemistry, 43, 407–435.CrossRef
Zurück zum Zitat Straub, J. E., & Thirumalai, D. (2010). Toward a molecular theory of early and late events in monomer to amyloid fibril formation. Annual Review of Physical Chemistry, 62, 437–463.CrossRef Straub, J. E., & Thirumalai, D. (2010). Toward a molecular theory of early and late events in monomer to amyloid fibril formation. Annual Review of Physical Chemistry, 62, 437–463.CrossRef
Zurück zum Zitat Sugita, Y. (2009). Free-energy landscapes of proteins in solution by generalized-ensemble simulations. Frontiers in Bioscience, 14, 1292–1303.CrossRef Sugita, Y. (2009). Free-energy landscapes of proteins in solution by generalized-ensemble simulations. Frontiers in Bioscience, 14, 1292–1303.CrossRef
Zurück zum Zitat Sugita, Y., & Okamoto, Y. (1999). Replica-exchange molecular dynamics method for protein folding. Chemical Physics Letters, 314, 141–151.CrossRef Sugita, Y., & Okamoto, Y. (1999). Replica-exchange molecular dynamics method for protein folding. Chemical Physics Letters, 314, 141–151.CrossRef
Zurück zum Zitat Sun, Q., Doerr, M., Li, Z., Smith, S. C., & Thiel, W. (2010). QM/MM studies of structural and energetic properties of the far-red fluorescent protein HcRed. Physical Chemistry Chemical Physics, 12(10), 2450–2458.CrossRef Sun, Q., Doerr, M., Li, Z., Smith, S. C., & Thiel, W. (2010). QM/MM studies of structural and energetic properties of the far-red fluorescent protein HcRed. Physical Chemistry Chemical Physics, 12(10), 2450–2458.CrossRef
Zurück zum Zitat Tajkhorshid, E., Aksimentiev, A., Balabin, I., Gao, M., Isralewitz, B., Phillips, J. C., et al. (2003). Large scale simulation of protein mechanics and function. Advances in Protein Chemistry, 66, 195–247.CrossRef Tajkhorshid, E., Aksimentiev, A., Balabin, I., Gao, M., Isralewitz, B., Phillips, J. C., et al. (2003). Large scale simulation of protein mechanics and function. Advances in Protein Chemistry, 66, 195–247.CrossRef
Zurück zum Zitat Tao, P., Hodošček, M., Larkin, J. D., Shao, Y., & Brooks, B. R. (2012). Comparison of three chain-of-states methods: Nudged elastic band and replica path with restraints or constraints. Journal of Chemical Theory and Computation, 8(12), 5035–5051.CrossRef Tao, P., Hodošček, M., Larkin, J. D., Shao, Y., & Brooks, B. R. (2012). Comparison of three chain-of-states methods: Nudged elastic band and replica path with restraints or constraints. Journal of Chemical Theory and Computation, 8(12), 5035–5051.CrossRef
Zurück zum Zitat Tatke, S. S., Loong, C. K., D’Souza, N., Schoephoerster, R. T., & Prabhakaran, M. (2008). Large scale motions in a biosensor protein glucose oxidase: A combined approach by DENS, normal mode analysis, and molecular dynamics studies. Biopolymers, 89(7), 582–594.CrossRef Tatke, S. S., Loong, C. K., D’Souza, N., Schoephoerster, R. T., & Prabhakaran, M. (2008). Large scale motions in a biosensor protein glucose oxidase: A combined approach by DENS, normal mode analysis, and molecular dynamics studies. Biopolymers, 89(7), 582–594.CrossRef
Zurück zum Zitat Tautermann, C. S., Seeliger, D., & Kriegl, J. M. (2015). What can we learn from molecular dynamics simulations for GPCR drug design? Computational and Structural Biotechnology Journal, 13, 111–121.CrossRef Tautermann, C. S., Seeliger, D., & Kriegl, J. M. (2015). What can we learn from molecular dynamics simulations for GPCR drug design? Computational and Structural Biotechnology Journal, 13, 111–121.CrossRef
Zurück zum Zitat Tekpinar, M., & Zheng, W. (2013). Coarse-grained and all-atom modeling of structural states and transitions in hemoglobin. Proteins, 81(2), 240–252.CrossRef Tekpinar, M., & Zheng, W. (2013). Coarse-grained and all-atom modeling of structural states and transitions in hemoglobin. Proteins, 81(2), 240–252.CrossRef
Zurück zum Zitat Towse, C.-L., & Daggett, V. (2013). Protein folding: Molecular dynamics simulations. In G. C. K. Roberts (Ed.), Encyclopedia of biophysics (pp. 2020–2025). Berlin/Heidelberg: Springer.CrossRef Towse, C.-L., & Daggett, V. (2013). Protein folding: Molecular dynamics simulations. In G. C. K. Roberts (Ed.), Encyclopedia of biophysics (pp. 2020–2025). Berlin/Heidelberg: Springer.CrossRef
Zurück zum Zitat Tozzini, V. (2010). Multiscale modeling of proteins. Accounts of Chemical Research, 43(2), 220–230.CrossRef Tozzini, V. (2010). Multiscale modeling of proteins. Accounts of Chemical Research, 43(2), 220–230.CrossRef
Zurück zum Zitat Trylska, J. (2010). Coarse-grained models to study dynamics of nanoscale biomolecules and their applications to the ribosome. Journal of Physics. Condensed Matter, 22(45), 453101.CrossRef Trylska, J. (2010). Coarse-grained models to study dynamics of nanoscale biomolecules and their applications to the ribosome. Journal of Physics. Condensed Matter, 22(45), 453101.CrossRef
Zurück zum Zitat Tsuduki, T., Tomita, A., Koshihara, S.-Y., Adachi, S.-I., & Yamato, T. (2012). Ligand migration in myoglobin: A combined study of computer simulation and x-ray crystallography. The Journal of Chemical Physics, 136(16), 165101.CrossRef Tsuduki, T., Tomita, A., Koshihara, S.-Y., Adachi, S.-I., & Yamato, T. (2012). Ligand migration in myoglobin: A combined study of computer simulation and x-ray crystallography. The Journal of Chemical Physics, 136(16), 165101.CrossRef
Zurück zum Zitat Urbanc, B., Betnel, M., Cruz, L., Bitan, G., & Teplow, D. B. (2010). Elucidation of amyloid beta-protein oligomerization mechanisms: Discrete molecular dynamics Study. Journal of the American Chemical Society, 132(12), 4266–4280.CrossRef Urbanc, B., Betnel, M., Cruz, L., Bitan, G., & Teplow, D. B. (2010). Elucidation of amyloid beta-protein oligomerization mechanisms: Discrete molecular dynamics Study. Journal of the American Chemical Society, 132(12), 4266–4280.CrossRef
Zurück zum Zitat Van Der Kamp, M. W., Shaw, K. E., Woods, C. J., & Mulholland, A. J. (2008). Biomolecular simulation and modelling: Status, progress and prospects. Journal of the Royal Society Interface, 5, 173–190.CrossRef Van Der Kamp, M. W., Shaw, K. E., Woods, C. J., & Mulholland, A. J. (2008). Biomolecular simulation and modelling: Status, progress and prospects. Journal of the Royal Society Interface, 5, 173–190.CrossRef
Zurück zum Zitat van der Kamp, M. W., Schaeffer, R. D., Jonsson, A. L., Scouras, A. D., Simms, A. M., Toofanny, R. D., et al. (2010). Dynameomics: A comprehensive database of protein dynamics. Structure, 18(4), 423–435. van der Kamp, M. W., Schaeffer, R. D., Jonsson, A. L., Scouras, A. D., Simms, A. M., Toofanny, R. D., et al. (2010). Dynameomics: A comprehensive database of protein dynamics. Structure, 18(4), 423–435.
Zurück zum Zitat Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718.CrossRef Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718.CrossRef
Zurück zum Zitat van der Vaart, A. (2015). Coupled binding–bending–folding: The complex conformational dynamics of protein-DNA binding studied by atomistic molecular dynamics simulations. Biochimica et Biophysica Acta (BBA) - General Subjects, 1850(5), 1091–1098.CrossRef van der Vaart, A. (2015). Coupled binding–bending–folding: The complex conformational dynamics of protein-DNA binding studied by atomistic molecular dynamics simulations. Biochimica et Biophysica Acta (BBA) - General Subjects, 1850(5), 1091–1098.CrossRef
Zurück zum Zitat Van Gunsteren, W. F., Bakowies, D., Baron, R., Chandrasekhar, I., Christen, M., Daura, X., Gee, P., Geerke, D. P., Glättli, A., Hünenberger, P. H., Kastenholz, M. A., Oostenbrink, C., Schenk, M., Trzesniak, D., Van Der Vegt, N. F. A., & Yu, H. B. (2006). Biomacromolecular modeling: Goals, problems, perspectives. Angewandte Chemie International Edition, 45,4064–4092.CrossRef Van Gunsteren, W. F., Bakowies, D., Baron, R., Chandrasekhar, I., Christen, M., Daura, X., Gee, P., Geerke, D. P., Glättli, A., Hünenberger, P. H., Kastenholz, M. A., Oostenbrink, C., Schenk, M., Trzesniak, D., Van Der Vegt, N. F. A., & Yu, H. B. (2006). Biomacromolecular modeling: Goals, problems, perspectives. Angewandte Chemie International Edition, 45,4064–4092.CrossRef
Zurück zum Zitat van Oijen, A. M. (2007). Single-molecule studies of complex systems: The replisome. Molecular BioSystems, 3(2), 117–125.CrossRef van Oijen, A. M. (2007). Single-molecule studies of complex systems: The replisome. Molecular BioSystems, 3(2), 117–125.CrossRef
Zurück zum Zitat van Speybroeck, V., & Meier, R. J. (2003). A recent development in computational chemistry: Chemical reactions from first principles molecular dynamics simulations. Chemical Society Reviews, 32(3), 151–157.CrossRef van Speybroeck, V., & Meier, R. J. (2003). A recent development in computational chemistry: Chemical reactions from first principles molecular dynamics simulations. Chemical Society Reviews, 32(3), 151–157.CrossRef
Zurück zum Zitat Vanommeslaeghe, K., & MacKerell, A. D., Jr. (2015). CHARMM additive and polarizable force fields for biophysics and computer-aided drug design. Biochimica et Biophysica Acta, 1850(5), 861–871.CrossRef Vanommeslaeghe, K., & MacKerell, A. D., Jr. (2015). CHARMM additive and polarizable force fields for biophysics and computer-aided drug design. Biochimica et Biophysica Acta, 1850(5), 861–871.CrossRef
Zurück zum Zitat Vargas, E., Yarov-Yarovoy, V., Khalili-Araghi, F., Catterall, W. A., Klein, M. L., Tarek, M., et al. (2012). An emerging consensus on voltage-dependent gating from computational modeling and molecular dynamics simulations. Journal of General Physiology, 140(6), 587–594.CrossRef Vargas, E., Yarov-Yarovoy, V., Khalili-Araghi, F., Catterall, W. A., Klein, M. L., Tarek, M., et al. (2012). An emerging consensus on voltage-dependent gating from computational modeling and molecular dynamics simulations. Journal of General Physiology, 140(6), 587–594.CrossRef
Zurück zum Zitat Vashisth, H., Skiniotis, G., & Brooks, C. L., 3rd. (2014). Collective variable approaches for single molecule flexible fitting and enhanced sampling. Chemical Reviews, 114(6), 3353–3365.CrossRef Vashisth, H., Skiniotis, G., & Brooks, C. L., 3rd. (2014). Collective variable approaches for single molecule flexible fitting and enhanced sampling. Chemical Reviews, 114(6), 3353–3365.CrossRef
Zurück zum Zitat Vasquez, V., Sotomayor, M., Cordero-Morales, J., Schulten, K., & Perozo, E. (2008). A structural mechanism for MscS gating in lipid bilayers. Science, 321(5893), 1210–1214.CrossRef Vasquez, V., Sotomayor, M., Cordero-Morales, J., Schulten, K., & Perozo, E. (2008). A structural mechanism for MscS gating in lipid bilayers. Science, 321(5893), 1210–1214.CrossRef
Zurück zum Zitat Vemparala, S., Domene, C., & Klein, M. L. (2010). Computational studies on the interactions of inhalational anesthetics with proteins. Accounts of Chemical Research, 43(1), 103–110.CrossRef Vemparala, S., Domene, C., & Klein, M. L. (2010). Computational studies on the interactions of inhalational anesthetics with proteins. Accounts of Chemical Research, 43(1), 103–110.CrossRef
Zurück zum Zitat Vicatos, S., Rychkova, A., Mukherjee, S., & Warshel, A. (2014). An effective coarse-grained model for biological simulations: Recent refinements and validations. Proteins, 82(7), 1168–1185.CrossRef Vicatos, S., Rychkova, A., Mukherjee, S., & Warshel, A. (2014). An effective coarse-grained model for biological simulations: Recent refinements and validations. Proteins, 82(7), 1168–1185.CrossRef
Zurück zum Zitat Villa, E., Balaeff, A., & Schulten, K. (2005). Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation. Proceedings of the National Academy of Sciences of the United States of America, 102(19), 6783–6788.CrossRef Villa, E., Balaeff, A., & Schulten, K. (2005). Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation. Proceedings of the National Academy of Sciences of the United States of America, 102(19), 6783–6788.CrossRef
Zurück zum Zitat Vuillon, L., & Lesieur, C. (2015). From local to global changes in proteins: A network view. Current Opinion in Structural Biology, 31, 1–8.CrossRef Vuillon, L., & Lesieur, C. (2015). From local to global changes in proteins: A network view. Current Opinion in Structural Biology, 31, 1–8.CrossRef
Zurück zum Zitat Wang, T., & Duan, Y. (2011). Retinal release from opsin in molecular dynamics simulations. Journal of Molecular Recognition, 24(2), 350–358.CrossRef Wang, T., & Duan, Y. (2011). Retinal release from opsin in molecular dynamics simulations. Journal of Molecular Recognition, 24(2), 350–358.CrossRef
Zurück zum Zitat Wang, P.-H., Bruschi, M., De Gioia, L., & Blumberger, J. (2013). Uncovering a dynamically formed substrate access tunnel in carbon monoxide dehydrogenase/acetyl-CoA synthase. Journal of the American Chemical Society, 135(25), 9493–9502.CrossRef Wang, P.-H., Bruschi, M., De Gioia, L., & Blumberger, J. (2013). Uncovering a dynamically formed substrate access tunnel in carbon monoxide dehydrogenase/acetyl-CoA synthase. Journal of the American Chemical Society, 135(25), 9493–9502.CrossRef
Zurück zum Zitat Wang, L. P., Martinez, T. J., & Pande, V. S. (2014). Building force fields: An automatic, systematic, and reproducible approach. Journal of Physical Chemistry Letters, 5(11), 1885–1891.CrossRef Wang, L. P., Martinez, T. J., & Pande, V. S. (2014). Building force fields: An automatic, systematic, and reproducible approach. Journal of Physical Chemistry Letters, 5(11), 1885–1891.CrossRef
Zurück zum Zitat Wanko, M., Hoffmann, M., Frauenheim, T., & Elstner, M. (2006). Computational photochemistry of retinal proteins. Journal of Computer-Aided Molecular Design, 20(7–8), 511–518.CrossRef Wanko, M., Hoffmann, M., Frauenheim, T., & Elstner, M. (2006). Computational photochemistry of retinal proteins. Journal of Computer-Aided Molecular Design, 20(7–8), 511–518.CrossRef
Zurück zum Zitat Warshel, A. (2002). Molecular dynamics simulations of biological reactions. Accounts of Chemical Research, 35(6), 385–395.CrossRef Warshel, A. (2002). Molecular dynamics simulations of biological reactions. Accounts of Chemical Research, 35(6), 385–395.CrossRef
Zurück zum Zitat Warshel, A. (2003). Computer simulations of enzyme catalysis: Methods, progress, and insights. Annual Review of Biophysics and Biomolecular Structure, 32, 425–443.CrossRef Warshel, A. (2003). Computer simulations of enzyme catalysis: Methods, progress, and insights. Annual Review of Biophysics and Biomolecular Structure, 32, 425–443.CrossRef
Zurück zum Zitat Warshel, A. (2014). Multiscale modeling of biological functions: From enzymes to molecular machines (Nobel lecture). Angewandte Chemie International Edition in English, 53(38), 10020–10031.CrossRef Warshel, A. (2014). Multiscale modeling of biological functions: From enzymes to molecular machines (Nobel lecture). Angewandte Chemie International Edition in English, 53(38), 10020–10031.CrossRef
Zurück zum Zitat Warshel, A., & Levitt, M. (1976). Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. Journal of Molecular Biology, 103(2), 227–249.CrossRef Warshel, A., & Levitt, M. (1976). Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. Journal of Molecular Biology, 103(2), 227–249.CrossRef
Zurück zum Zitat Warshel, A., Levitt, M., & Lifson, S. (1970). Consistent force field for calculation of vibrational spectra and conformations of some amides and lactam rings. Journal of Molecular Spectroscopy, 33(1), 84–99.CrossRef Warshel, A., Levitt, M., & Lifson, S. (1970). Consistent force field for calculation of vibrational spectra and conformations of some amides and lactam rings. Journal of Molecular Spectroscopy, 33(1), 84–99.CrossRef
Zurück zum Zitat Warshel, A., Kato, M., & Pisliakov, A. V. (2007). Polarizable force fields: History, test cases, and prospects. Journal of Chemical Theory and Computation, 3(6), 2034–2045.CrossRef Warshel, A., Kato, M., & Pisliakov, A. V. (2007). Polarizable force fields: History, test cases, and prospects. Journal of Chemical Theory and Computation, 3(6), 2034–2045.CrossRef
Zurück zum Zitat Weber, D. K., Yao, S., Rojko, N., Anderluh, G., Lybrand, T. P., Downton, M. T., et al. (2015). Characterization of the lipid-binding site of equinatoxin ii by nmr and molecular dynamics simulation. Biophysical Journal, 108(8), 1987–1996.CrossRef Weber, D. K., Yao, S., Rojko, N., Anderluh, G., Lybrand, T. P., Downton, M. T., et al. (2015). Characterization of the lipid-binding site of equinatoxin ii by nmr and molecular dynamics simulation. Biophysical Journal, 108(8), 1987–1996.CrossRef
Zurück zum Zitat Weiner, S. J., Kollman, P. A., Case, D. A., Singh, U. C., Ghio, C., Alagona, G., et al. (1984). A new force-field for molecular mechanical simulation of nucleic-acids and proteins. Journal of the American Chemical Society, 106(3), 765–784.CrossRef Weiner, S. J., Kollman, P. A., Case, D. A., Singh, U. C., Ghio, C., Alagona, G., et al. (1984). A new force-field for molecular mechanical simulation of nucleic-acids and proteins. Journal of the American Chemical Society, 106(3), 765–784.CrossRef
Zurück zum Zitat Wong, V., & Case, D. A. (2008). Evaluating rotational diffusion from protein MD simulations. Journal of Physical Chemistry B, 112(19), 6013–6024.CrossRef Wong, V., & Case, D. A. (2008). Evaluating rotational diffusion from protein MD simulations. Journal of Physical Chemistry B, 112(19), 6013–6024.CrossRef
Zurück zum Zitat Wright, P. E., & Dyson, H. J. (1999). Intrinsically unstructured proteins: Re-assessing the protein structure-function paradigm. Journal of Molecular Biology, 293(2), 321–331.CrossRef Wright, P. E., & Dyson, H. J. (1999). Intrinsically unstructured proteins: Re-assessing the protein structure-function paradigm. Journal of Molecular Biology, 293(2), 321–331.CrossRef
Zurück zum Zitat Wright, P. E., & Dyson, H. J. (2015). Intrinsically disordered proteins in cellular signalling and regulation. Nature Reviews Molecular Cell Biology, 16(1), 18–29.CrossRef Wright, P. E., & Dyson, H. J. (2015). Intrinsically disordered proteins in cellular signalling and regulation. Nature Reviews Molecular Cell Biology, 16(1), 18–29.CrossRef
Zurück zum Zitat Yu, J., Ha, T., & Schulten, K. (2007). How directional translocation is regulated in a DNA helicase motor. Biophysical Journal, 93(11), 3783–3797.CrossRef Yu, J., Ha, T., & Schulten, K. (2007). How directional translocation is regulated in a DNA helicase motor. Biophysical Journal, 93(11), 3783–3797.CrossRef
Zurück zum Zitat Yuriev, E., Holien, J., & Ramsland, P. A. (2015). Improvements, trends, and new ideas in molecular docking: 2012–2013 in review. Journal of Molecular Recognition, 28(10), 581–604.CrossRef Yuriev, E., Holien, J., & Ramsland, P. A. (2015). Improvements, trends, and new ideas in molecular docking: 2012–2013 in review. Journal of Molecular Recognition, 28(10), 581–604.CrossRef
Zurück zum Zitat Zerze, G. I. H., Miller, C. M., Granata, D., & Mittal, J. (2015). Free energy surface of an intrinsically disordered protein: Comparison between temperature replica exchange molecular dynamics and bias-exchange metadynamics. Journal of Chemical Theory and Computation, 11(6), 2776–2782.CrossRef Zerze, G. I. H., Miller, C. M., Granata, D., & Mittal, J. (2015). Free energy surface of an intrinsically disordered protein: Comparison between temperature replica exchange molecular dynamics and bias-exchange metadynamics. Journal of Chemical Theory and Computation, 11(6), 2776–2782.CrossRef
Zurück zum Zitat Zhang, J., Li, W., Wang, J., Qin, M., Wu, L., Yan, Z., et al. (2009). Protein folding simulations: From coarse-grained model to all-atom model. IUBMB Life, 61(6), 627–643.CrossRef Zhang, J., Li, W., Wang, J., Qin, M., Wu, L., Yan, Z., et al. (2009). Protein folding simulations: From coarse-grained model to all-atom model. IUBMB Life, 61(6), 627–643.CrossRef
Zurück zum Zitat Zhang, L., Lua, L. H. L., Middelberg, A. P. J., Sun, Y., & Connors, N. K. (2015). Biomolecular engineering of virus-like particles aided by computational chemistry methods. Chemical Society Reviews, 44(23), 8608–8618. doi:10.1039/C5CS00526D. Zhang, L., Lua, L. H. L., Middelberg, A. P. J., Sun, Y., & Connors, N. K. (2015). Biomolecular engineering of virus-like particles aided by computational chemistry methods. Chemical Society Reviews, 44(23), 8608–8618. doi:10.1039/C5CS00526D.
Zurück zum Zitat Zhao, H., & Caflisch, A. (2015). Molecular dynamics in drug design. European Journal of Medicinal Chemistry, 91, 4–14.CrossRef Zhao, H., & Caflisch, A. (2015). Molecular dynamics in drug design. European Journal of Medicinal Chemistry, 91, 4–14.CrossRef
Zurück zum Zitat Zhao, G., Perilla, J. R., Yufenyuy, E. L., Meng, X., Chen, B., Ning, J., et al. (2013). Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Nature, 497(7451), 643–646.CrossRef Zhao, G., Perilla, J. R., Yufenyuy, E. L., Meng, X., Chen, B., Ning, J., et al. (2013). Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Nature, 497(7451), 643–646.CrossRef
Zurück zum Zitat Zhmurov, A., Dima, R. I., Kholodov, Y., & Barsegov, V. (2010). Sop-GPU: Accelerating biomolecular simulations in the centisecond timescale using graphics processors. Proteins, 78(14), 2984–2999.CrossRef Zhmurov, A., Dima, R. I., Kholodov, Y., & Barsegov, V. (2010). Sop-GPU: Accelerating biomolecular simulations in the centisecond timescale using graphics processors. Proteins, 78(14), 2984–2999.CrossRef
Zurück zum Zitat Zink, M., & Grubmuller, H. (2009). Mechanical properties of the Icosahedral shell of southern bean mosaic virus: A molecular dynamics study. Biophysical Journal, 96(4), 1350–1363.CrossRef Zink, M., & Grubmuller, H. (2009). Mechanical properties of the Icosahedral shell of southern bean mosaic virus: A molecular dynamics study. Biophysical Journal, 96(4), 1350–1363.CrossRef
Zurück zum Zitat Zoete, V., Cuendet, M. A., Grosdidier, A., & Michielin, O. (2011). SwissParam: A fast force field generation tool for small organic molecules. Journal of Computational Chemistry, 32(11), 2359–2368.CrossRef Zoete, V., Cuendet, M. A., Grosdidier, A., & Michielin, O. (2011). SwissParam: A fast force field generation tool for small organic molecules. Journal of Computational Chemistry, 32(11), 2359–2368.CrossRef
Zurück zum Zitat Zwier, M. C., Adelman, J. L., Kaus, J. W., Pratt, A. J., Wong, K. F., Rego, N. B., et al. (2015). WESTPA: An interoperable, highly scalable software package for weighted ensemble simulation and analysis. Journal of Chemical Theory and Computation, 11(2), 800–809.CrossRef Zwier, M. C., Adelman, J. L., Kaus, J. W., Pratt, A. J., Wong, K. F., Rego, N. B., et al. (2015). WESTPA: An interoperable, highly scalable software package for weighted ensemble simulation and analysis. Journal of Chemical Theory and Computation, 11(2), 800–809.CrossRef
Metadaten
Titel
Applications of Computational Methods to Simulations of Proteins Dynamics
verfasst von
Wieslaw Nowak
Copyright-Jahr
2017
DOI
https://doi.org/10.1007/978-3-319-27282-5_31