Skip to main content
Disciplines
Automotive Business IT + Informatics Construction + Real Estate Electrical Engineering + Electronics Energy + Sustainability Insurance + Risk Finance + Banking Management + Leadership Marketing + Sales Mechanical Engineering + Materials
Events
DE
EN
Books
Journals
Topic Page
Marketing
Start single access now
Access for companies
EXTENDED SEARCH
Log in
Top
Published in:
Discrete Energy Laws for the First-Order System Least-Squares Finite-Element Approach Read chapter Read first chapter

2018 | OriginalPaper | Chapter

Sampling in In Silico Biomolecular Studies: Single-Stage Experiments vs Multiscale Approaches

Authors : Nevena Ilieva, Jiaojiao Liu, Xubiao Peng, Jianfeng He, Antti Niemi, Peicho Petkov, Leandar Litov

Published in: Large-Scale Scientific Computing

Publisher: Springer International Publishing

Log in

Activate our intelligent search to find suitable subject content or patents.

search-config
loading …

Abstract

In silico studies of biological molecules face the problem of sampling quality due to the systems size (in atom numbers), the time scale of the investigated processes and the admissible computational time step. Advances in hardware alone are incapable of resolving this problem and the efforts are oriented towards sampling techniques enhancements, multilevel system representations and development of multistage and multiscale methods through synergistic protocols from complementary approaches. We combine a mean field approach with all atom molecular dynamics (MD), to develop a multistage algorithm that can model protein folding and dynamics over very long time periods with atomic-level precision. We compare the quality of conformation-space sampling for villin headpiece (PDB ID 2F4K) with a 125 \(\upmu \)s long folding simulation performed on the dedicated supercomputer ANTON.

Dont have a licence yet? Then find out more about our products and how to get one now:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

  • über 102.000 Bücher
  • über 537 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Maschinenbau + Werkstoffe
  • Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

inform now

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 390 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Maschinenbau + Werkstoffe




 

Jetzt Wissensvorsprung sichern!

inform now

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 340 Zeitschriften

aus folgenden Fachgebieten:

  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Versicherung + Risiko




Jetzt Wissensvorsprung sichern!

inform now
previous chapter A Domain Decomposition Multilevel Preconditioner for Interpolation with Radial Basis Functions
next chapter Cultural Heritage RC Structures Environmentally Degradated: Optimal Seismic Upgrading by Tention-Ties Under Shear Effects
Literature
1.
Bazari, W.L., Matsudaira, P., Wallek, M., Smeal, T., Jakes, R., Ahmed, Y.: Villin sequence and peptide map identify six homologous domains. Proc. Natl. Acad. Sci. U.S.A. 85, 4986–4990 (1988)CrossRef
2.
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The protein data bank. Nucleic Acids Res. 28(1), 235–242 (2000)CrossRef
3.
Chernodub, M., Hu, S., Niemi, A.J.: Topological solitons and folded proteins. Phys. Rev. E 82, 011916 (2010)CrossRef
4.
Chiu, T.K., Kubelka, J., Herbst-Irmer, R., Eaton, W.A., Hofrichter, J., Davies, D.R.: High-resolution x-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein. Proc. Natl. Acad. Sci. U.S.A. 102, 7517–7522 (2005)CrossRef
5.
Dai, J., Niemi, A., He, J., Sieradzan, A., Ilieva, N.: Bloch spin waves and emergent structure in protein folding with hiv envelope glycoprotein as an example. Phys. Rev. E 93, 032409 (2016)CrossRef
6.
Frenkel, D., Smit, B.: Understanding Molecular Simulation. Academic Press, Cambridge (2001)MATH
7.
Gelman, H., Gruebele, M.: Fast protein folding kinetics. Q. Rev. Biophys. 47(2), 95–142 (2014)CrossRef
8.
Ilieva, N., Liu, J., Marinova, R., Petkov, P., Litov, L., He, J., Niemi, A.J.: Are there folding pathways in the functional stages of intrinsically disordered proteins? In: AIP Conference Proceedings, vol. 1773, no. 1, p. 110008 (2016)
9.
Jennings, P., Wright, P.: Formation of a molten globule intermediate early in the kinetic folding pathway of apomyoglobin. Science 262, 892–896 (1993)CrossRef
10.
Krokhotin, A., Lundgren, M., Niemi, A.J., Peng, X.: Soliton driven relaxation dynamics and protein collapse in the villin headpiece. J. Phys.: Condens. Matter 25(32), 325103 (2013)
11.
Kubelka, J., Chiu, T., Davies, D., Eaton, W., Hofrichter, J.: Sub-microsecond protein folding. J. Mol. Biol. 359, 546–553 (2006)CrossRef
12.
Lindorff-Larsen, K., Piana, S., Dror, R.O., Shaw, D.E.: How fast-folding proteins fold. Science 334(6055), 517–520 (2011)CrossRef
13.
Liu, J., Dai, J., He, J., Niemi, A.J., Ilieva, N.: Multistage modeling of protein dynamics with monomeric Myc oncoprotein as an example. Phys. Rev. E 95, 032406 (2017)CrossRef
14.
Metropolis, N., Rosenbluth, A., Rosenbluth, M., Teller, A., Teller, E.: Equation of state calculations by fast computing machines. J. Chem. Phys. 21(6), 1087–1092 (1953)CrossRef
15.
16.
17.
Raval, A., Piana, S., Eastwood, M.P., Dror, R.O., Shaw, D.E.: Refinement of protein structure homology models via long, all-atom molecular dynamics simulations. Proteins: Struct. Funct. Bioinf. 80(8), 2071–2079 (2012)
18.
Rotkiewicz, P., Skolnick, J.: Fast procedure for reconstruction of full-atom protein models from reduced representations. J. Comput. Chem. 29(9), 1460–1465 (2008)CrossRef
19.
20.
Saunders, M., Voth, G.: Coarse-graining methods for computational biology. Annu. Rev. Biophys. 42, 73–93 (2013)CrossRef
21.
Shaw, D.E., et al.: Anton, a special-purpose machine for molecular dynamics simulation. SIGARCH Comput. Archit. News 35(2), 1–12 (2007)MathSciNetCrossRef
22.
Shaw, D.E., et al.: Millisecond-scale molecular dynamics simulations on Anton. In: Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis, SC 2009, pp. 39:1–39:11. ACM, New York (2009)
Metadata
Title
Sampling in In Silico Biomolecular Studies: Single-Stage Experiments vs Multiscale Approaches
Authors
Nevena Ilieva
Jiaojiao Liu
Xubiao Peng
Jianfeng He
Antti Niemi
Peicho Petkov
Leandar Litov
Copyright Year
2018
Book
Large-Scale Scientific Computing

Print ISBN: 978-3-319-73440-8

Electronic ISBN: 978-3-319-73441-5

Copyright Year: 2018

DOI
https://doi.org/10.1007/978-3-319-73441-5_56

Premium Partner

    Image Credits