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2014 | OriginalPaper | Buchkapitel

11. Protein Modeling and Structural Prediction

verfasst von : Sebastian Kelm, Yoonjoo Choi, Charlotte M. Deane

Erschienen in: Springer Handbook of Bio-/Neuroinformatics

Verlag: Springer Berlin Heidelberg

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Abstract

Proteins perform crucial functions in every living cell. The genetic information in every organismʼs DNA encodes the proteinʼs amino acid sequence, which determines its three-dimensional structure, which, in turn, determines its function. In this postgenomic era, protein sequence information can be obtained relatively easily through experimental means. Sequence databases already contain millions of protein sequences and continue to grow. Structural information, however, is harder to obtain through experimental means – we currently know the structure of about 75000 proteins. Knowledge of a proteinʼs structure is extremely useful in understanding its molecular function and in developing drugs that bind to it. Thus, computational techniques have been developed to bridge the ever-increasing gap between the number of known protein sequences and structures.
In addition to proteins in general, this chapter discusses the specific importance of membrane proteins, which make up about one-third of all known proteins. Membrane proteins control communication and transport into and out of every living cell and are involved in many medically important processes. Over half of current drug targets are membrane proteins.
A brief introduction to protein sequence and structure is followed by an overview of common techniques used in the process of computational protein structure prediction. Emphasis is put on two particularly hard problems, namely protein loop modeling and the structural prediction of membrane proteins.

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Literatur
11.1.
Zurück zum Zitat B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Robets, P. Walter: Molecular Biology of the Cell, 4th edn. (Garland Science, New York 2002) B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Robets, P. Walter: Molecular Biology of the Cell, 4th edn. (Garland Science, New York 2002)
11.2.
Zurück zum Zitat R.A. Laskowski, M.W. MacArthur, D.S. Moss, J.M. Thornton: PROCHECK: A program to check the stereochemical quality of protein structures, J. Appl. Cryst. 26, 283–291 (1993)CrossRef R.A. Laskowski, M.W. MacArthur, D.S. Moss, J.M. Thornton: PROCHECK: A program to check the stereochemical quality of protein structures, J. Appl. Cryst. 26, 283–291 (1993)CrossRef
11.3.
Zurück zum Zitat C.B. Anfinsen: Principles that govern the folding of protein chains, Science 181(96), 223–230 (1973)CrossRef C.B. Anfinsen: Principles that govern the folding of protein chains, Science 181(96), 223–230 (1973)CrossRef
11.4.
Zurück zum Zitat C. Ramakrishnan, G.N. Ramachandran: Stereochemical criteria for polypeptide and protein chain conformations: II. Allowed conformations for a pair of peptide units, Biophys. J. 5, 909–933 (1965)CrossRef C. Ramakrishnan, G.N. Ramachandran: Stereochemical criteria for polypeptide and protein chain conformations: II. Allowed conformations for a pair of peptide units, Biophys. J. 5, 909–933 (1965)CrossRef
11.5.
Zurück zum Zitat W. Kabsch, C. Sander: Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features, Biopolymers 22(12), 2577–2637 (1983)CrossRef W. Kabsch, C. Sander: Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features, Biopolymers 22(12), 2577–2637 (1983)CrossRef
11.6.
Zurück zum Zitat J.M. Berg, J.L. Tymoczko, L. Stryer: Biochemistry, 5th edn. (Freeman, New York 2002) J.M. Berg, J.L. Tymoczko, L. Stryer: Biochemistry, 5th edn. (Freeman, New York 2002)
11.7.
Zurück zum Zitat G. von Heijne: The membrane protein universe: Whatʼs out there and why bother?, J. Intern. Med. 261(6), 543–557 (2007)CrossRef G. von Heijne: The membrane protein universe: Whatʼs out there and why bother?, J. Intern. Med. 261(6), 543–557 (2007)CrossRef
11.8.
Zurück zum Zitat D.J. Müller, N. Wu, K. Palczewski: Vertebrate membrane proteins: Structure, function, and insights from biophysical approaches, Pharmacol. Rev. 60(1), 43–78 (2008)CrossRef D.J. Müller, N. Wu, K. Palczewski: Vertebrate membrane proteins: Structure, function, and insights from biophysical approaches, Pharmacol. Rev. 60(1), 43–78 (2008)CrossRef
11.9.
Zurück zum Zitat S. Henikoff, J.G. Henikoff: Amino acid substitution matrices from protein blocks, Proc. Natl. Acad. Sci. USA 89(22), 10915–10919 (1992)CrossRef S. Henikoff, J.G. Henikoff: Amino acid substitution matrices from protein blocks, Proc. Natl. Acad. Sci. USA 89(22), 10915–10919 (1992)CrossRef
11.10.
Zurück zum Zitat D.T. Jones, W.R. Taylor, J.M. Thornton: A model recognition approach to the prediction of all-helical membrane protein structure and topology, Biochemistry 33(10), 3038–3049 (1994)CrossRef D.T. Jones, W.R. Taylor, J.M. Thornton: A model recognition approach to the prediction of all-helical membrane protein structure and topology, Biochemistry 33(10), 3038–3049 (1994)CrossRef
11.11.
Zurück zum Zitat P. Ng, J. Henikoff, S. Henikoff: PHAT: A transmembrane-specific substitution matrix, Bioinformatics 16(9), 760–766 (2000)CrossRef P. Ng, J. Henikoff, S. Henikoff: PHAT: A transmembrane-specific substitution matrix, Bioinformatics 16(9), 760–766 (2000)CrossRef
11.12.
Zurück zum Zitat T. Müller, S. Rahmann, M. Rehmsmeier: Non-symmetric score matrices and the detection of homologous transmembrane proteins, Bioinformatics 17(1), S182–S189 (2001)CrossRef T. Müller, S. Rahmann, M. Rehmsmeier: Non-symmetric score matrices and the detection of homologous transmembrane proteins, Bioinformatics 17(1), S182–S189 (2001)CrossRef
11.13.
Zurück zum Zitat J. Shi, T.L. Blundell, K. Mizuguchi: FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties, J. Mol. Biol. 310(1), 243–257 (2001)CrossRef J. Shi, T.L. Blundell, K. Mizuguchi: FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties, J. Mol. Biol. 310(1), 243–257 (2001)CrossRef
11.14.
Zurück zum Zitat J.R. Hill, S. Kelm, J. Shi, C.M. Deane: Environment specific substitution tables improve membrane protein alignment, Bioinformatics 27(13), i15–i23 (2011)CrossRef J.R. Hill, S. Kelm, J. Shi, C.M. Deane: Environment specific substitution tables improve membrane protein alignment, Bioinformatics 27(13), i15–i23 (2011)CrossRef
11.15.
Zurück zum Zitat A. Kryshtafovych, C. Venclovas, K. Fidelis, J. Moult: Progress over the first decade of CASP experiments, Proteins 61(7), 225–236 (2005)CrossRef A. Kryshtafovych, C. Venclovas, K. Fidelis, J. Moult: Progress over the first decade of CASP experiments, Proteins 61(7), 225–236 (2005)CrossRef
11.16.
Zurück zum Zitat J. Moult, K. Fidelis, A. Kryshtafovych, B. Rost, T. Hubbard, A. Tramontano: Critical assessment of methods of protein structure prediction – Round VII, Proteins 69, 3–9 (2007)CrossRef J. Moult, K. Fidelis, A. Kryshtafovych, B. Rost, T. Hubbard, A. Tramontano: Critical assessment of methods of protein structure prediction – Round VII, Proteins 69, 3–9 (2007)CrossRef
11.17.
Zurück zum Zitat J. Moult, K. Fidelis, A. Kryshtafovych, B. Rost, A. Tramontano: Critical assessment of methods of protein structure prediction – Round VIII, Proteins 9(77), 1–4 (2009)CrossRef J. Moult, K. Fidelis, A. Kryshtafovych, B. Rost, A. Tramontano: Critical assessment of methods of protein structure prediction – Round VIII, Proteins 9(77), 1–4 (2009)CrossRef
11.18.
Zurück zum Zitat C.M. Deane, M. Dong, F.P. Huard, B.K. Lance, G.R. Wood: Cotranslational protein folding – fact or fiction?, Bioinformatics 23(13), i142–i148 (2007)CrossRef C.M. Deane, M. Dong, F.P. Huard, B.K. Lance, G.R. Wood: Cotranslational protein folding – fact or fiction?, Bioinformatics 23(13), i142–i148 (2007)CrossRef
11.19.
Zurück zum Zitat J.J. Ellis, F.P.P. Huard, C.M. Deane, S. Srivastava, G.R. Wood: Directionality in protein fold prediction, BMC Bioinformatics 11(1), 172 (2010)CrossRef J.J. Ellis, F.P.P. Huard, C.M. Deane, S. Srivastava, G.R. Wood: Directionality in protein fold prediction, BMC Bioinformatics 11(1), 172 (2010)CrossRef
11.20.
Zurück zum Zitat B.R. Jefferys, L.A. Kelley, M.J.E. Sternberg: Protein folding requires crowd control in a simulated cell, J. Mol. Biol. 397(5), 1329–1338 (2010)CrossRef B.R. Jefferys, L.A. Kelley, M.J.E. Sternberg: Protein folding requires crowd control in a simulated cell, J. Mol. Biol. 397(5), 1329–1338 (2010)CrossRef
11.21.
Zurück zum Zitat R. Das, D. Baker: Macromolecular modeling with rosetta, Annu. Rev. Biochem. 77(1), 363–382 (2008)CrossRef R. Das, D. Baker: Macromolecular modeling with rosetta, Annu. Rev. Biochem. 77(1), 363–382 (2008)CrossRef
11.22.
Zurück zum Zitat K.T. Simons, R. Bonneau, I. Ruczinski, D. Baker: Ab initio protein structure prediction of CASP III targets using ROSETTA, Proteins 37(3), 171–176 (1999)CrossRef K.T. Simons, R. Bonneau, I. Ruczinski, D. Baker: Ab initio protein structure prediction of CASP III targets using ROSETTA, Proteins 37(3), 171–176 (1999)CrossRef
11.23.
Zurück zum Zitat P. Bradley, L. Malmström, B. Qian, J. Schonbrun, D. Chivian, D.E. Kim, J. Meiler, K.M.S. Misura, D. Baker: Free modeling with Rosetta in CASP6, Proteins 61(7), 128–134 (2005)CrossRef P. Bradley, L. Malmström, B. Qian, J. Schonbrun, D. Chivian, D.E. Kim, J. Meiler, K.M.S. Misura, D. Baker: Free modeling with Rosetta in CASP6, Proteins 61(7), 128–134 (2005)CrossRef
11.24.
Zurück zum Zitat R. Das, B. Qian, S. Raman, R. Vernon, J. Thompson, P. Bradley, S. Khare, M.D. Tyka, D. Bhat, D. Chivian, D.E. Kim, W.H. Sheffler, L. Malmström, A.M. Wollacott, C. Wang, I. Andre, D. Baker: Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home, Proteins 69(S8), 118–128 (2007)CrossRef R. Das, B. Qian, S. Raman, R. Vernon, J. Thompson, P. Bradley, S. Khare, M.D. Tyka, D. Bhat, D. Chivian, D.E. Kim, W.H. Sheffler, L. Malmström, A.M. Wollacott, C. Wang, I. Andre, D. Baker: Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home, Proteins 69(S8), 118–128 (2007)CrossRef
11.25.
Zurück zum Zitat S.F. Altschul, W. Gish, W. Miller, E.W. Myers, D.J. Lipman: Basic local alignment search tool, J. Mol. Biol. 215(3), 403–410 (1990)CrossRef S.F. Altschul, W. Gish, W. Miller, E.W. Myers, D.J. Lipman: Basic local alignment search tool, J. Mol. Biol. 215(3), 403–410 (1990)CrossRef
11.26.
Zurück zum Zitat J. Söding, A. Biegert, A. Lupas: The HHpred interactive server for protein homology detection and structure prediction, Nucleic Acids Res. 33(2), W244–W248 (2005)CrossRef J. Söding, A. Biegert, A. Lupas: The HHpred interactive server for protein homology detection and structure prediction, Nucleic Acids Res. 33(2), W244–W248 (2005)CrossRef
11.27.
Zurück zum Zitat C.M. Deane: Protein Structure Prediction: Amino Acid Propensities and Comparative Modelling (Univ. of Cambridge, Cambridge 2000) C.M. Deane: Protein Structure Prediction: Amino Acid Propensities and Comparative Modelling (Univ. of Cambridge, Cambridge 2000)
11.28.
Zurück zum Zitat R. Sánchez, A. Sali: Advances in comparative protein-structure modelling, Curr. Opin. Struct. Biol. 7(2), 206–214 (1997)CrossRef R. Sánchez, A. Sali: Advances in comparative protein-structure modelling, Curr. Opin. Struct. Biol. 7(2), 206–214 (1997)CrossRef
11.29.
Zurück zum Zitat A. Sali, T.L. Blundell: Comparative protein modelling by satisfaction of spatial restraints, J. Mol. Biol. 234(3), 779–815 (1993)CrossRef A. Sali, T.L. Blundell: Comparative protein modelling by satisfaction of spatial restraints, J. Mol. Biol. 234(3), 779–815 (1993)CrossRef
11.30.
Zurück zum Zitat M.J. Sutcliffe, I. Haneef, D. Carney, T.L. Blundell: Knowledge based modelling of homologous proteins, Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures, Protein Eng. 1(5), 377–384 (1987)CrossRef M.J. Sutcliffe, I. Haneef, D. Carney, T.L. Blundell: Knowledge based modelling of homologous proteins, Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures, Protein Eng. 1(5), 377–384 (1987)CrossRef
11.31.
Zurück zum Zitat P.A. Bates, L.A. Kelley, R.M. MacCallum, M.J. Sternberg: Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM, Proteins 45(5), 39–46 (2001)CrossRef P.A. Bates, L.A. Kelley, R.M. MacCallum, M.J. Sternberg: Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM, Proteins 45(5), 39–46 (2001)CrossRef
11.32.
Zurück zum Zitat T. Schwede, J. Kopp, N. Guex, M.C. Peitsch: SWISS-MODEL: An automated protein homology-modeling server, Nucleic Acids Res. 31(13), 3381–3385 (2003)CrossRef T. Schwede, J. Kopp, N. Guex, M.C. Peitsch: SWISS-MODEL: An automated protein homology-modeling server, Nucleic Acids Res. 31(13), 3381–3385 (2003)CrossRef
11.33.
Zurück zum Zitat D. Petrey, Z. Xiang, C.L. Tang, L. Xie, M. Gimpelev, T. Mitros, C.S. Soto, S. Goldsmith-Fischman, A. Kernytsky, A. Schlessinger, I.Y. Koh, E. Alexov, B. Honig: Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling, Proteins 53(6), 430–435 (2003)CrossRef D. Petrey, Z. Xiang, C.L. Tang, L. Xie, M. Gimpelev, T. Mitros, C.S. Soto, S. Goldsmith-Fischman, A. Kernytsky, A. Schlessinger, I.Y. Koh, E. Alexov, B. Honig: Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling, Proteins 53(6), 430–435 (2003)CrossRef
11.34.
Zurück zum Zitat C.M. Deane, T.L. Blundell: CODA: A combined algorithm for predicting the structurally variable regions of protein models, Protein Sci. 10(3), 599–612 (2001)CrossRef C.M. Deane, T.L. Blundell: CODA: A combined algorithm for predicting the structurally variable regions of protein models, Protein Sci. 10(3), 599–612 (2001)CrossRef
11.35.
Zurück zum Zitat P. Koehl, M. Delarue: A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modelling, Nat. Struct. Biol. 2(2), 163–170 (1995)CrossRef P. Koehl, M. Delarue: A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modelling, Nat. Struct. Biol. 2(2), 163–170 (1995)CrossRef
11.36.
Zurück zum Zitat G.G. Krivov, V.M. Shapovalov, L.R. Dunbrack: Improved prediction of protein side-chain conformations with SCWRL4, Proteins 77(4), 778–795 (2009)CrossRef G.G. Krivov, V.M. Shapovalov, L.R. Dunbrack: Improved prediction of protein side-chain conformations with SCWRL4, Proteins 77(4), 778–795 (2009)CrossRef
11.37.
Zurück zum Zitat L.E. Donate, S.D. Rufino, L.H.J. Canard, T.L. Blundell: Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: A database for modeling and prediction, Protein Sci. 5, 2600–2616 (1996)CrossRef L.E. Donate, S.D. Rufino, L.H.J. Canard, T.L. Blundell: Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: A database for modeling and prediction, Protein Sci. 5, 2600–2616 (1996)CrossRef
11.38.
Zurück zum Zitat G.D. Rose: Prediction of chain turns in globular proteins on a hydrophobic basis, Nature 272, 586–590 (1978)CrossRef G.D. Rose: Prediction of chain turns in globular proteins on a hydrophobic basis, Nature 272, 586–590 (1978)CrossRef
11.39.
Zurück zum Zitat I.P. Crawford, T. Niermann, K. Kirschner: Prediction of secondary structure by evolutionary comparison: Application to the α subunit of tryptophan synthase, Proteins 2(2), 118–129 (1987)CrossRef I.P. Crawford, T. Niermann, K. Kirschner: Prediction of secondary structure by evolutionary comparison: Application to the α subunit of tryptophan synthase, Proteins 2(2), 118–129 (1987)CrossRef
11.40.
Zurück zum Zitat J. Wojcik, J.-P. Mornon, J. Chomilier: New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification, J. Mol. Biol. 289, 1469–1490 (1999)CrossRef J. Wojcik, J.-P. Mornon, J. Chomilier: New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification, J. Mol. Biol. 289, 1469–1490 (1999)CrossRef
11.41.
Zurück zum Zitat N. Fernandez-Fuentes, B. Olivia, A. Fiser: A supersecondary structure library and search algorithm for modeling loops in protein structures, Nucleic Acids Res. 34, 2085–2097 (2006)CrossRef N. Fernandez-Fuentes, B. Olivia, A. Fiser: A supersecondary structure library and search algorithm for modeling loops in protein structures, Nucleic Acids Res. 34, 2085–2097 (2006)CrossRef
11.42.
Zurück zum Zitat N. Fernandez-Fuentes, J. Zhai, A. Fiser: ArchPRED: A template based loop structure prediction server, Nucleic Acids Res. 34, W173–W176 (2006)CrossRef N. Fernandez-Fuentes, J. Zhai, A. Fiser: ArchPRED: A template based loop structure prediction server, Nucleic Acids Res. 34, W173–W176 (2006)CrossRef
11.43.
Zurück zum Zitat E. Michalsky, A. Goede, R. Preissner: Loops in proteins (LIP) – a comprehensive loop database for homology modeling, Protein Eng. 16, 979–985 (2003)CrossRef E. Michalsky, A. Goede, R. Preissner: Loops in proteins (LIP) – a comprehensive loop database for homology modeling, Protein Eng. 16, 979–985 (2003)CrossRef
11.44.
Zurück zum Zitat A. Hildebrand, M. Remmert, A. Biegert, J. Söding: Fast and accurate automatic structure prediction with HHpred, Proteins 77(S9), 128–132 (2009)CrossRef A. Hildebrand, M. Remmert, A. Biegert, J. Söding: Fast and accurate automatic structure prediction with HHpred, Proteins 77(S9), 128–132 (2009)CrossRef
11.45.
Zurück zum Zitat H. Peng, A. Yang: Modeling protein loops with knowledge-based prediction of sequence-structure alignment, Bioinformatics 23, 2836–2842 (2007)MathSciNetCrossRef H. Peng, A. Yang: Modeling protein loops with knowledge-based prediction of sequence-structure alignment, Bioinformatics 23, 2836–2842 (2007)MathSciNetCrossRef
11.46.
Zurück zum Zitat Y. Choi, C.M. Deane: FREAD revisited: Accurate loop structure prediction using a database search algorithm, Proteins 78(6), 1431–1440 (2010) Y. Choi, C.M. Deane: FREAD revisited: Accurate loop structure prediction using a database search algorithm, Proteins 78(6), 1431–1440 (2010)
11.47.
Zurück zum Zitat C.M. Deane, T.L. Blundell: A novel exhaustive search algorithm for predicting the conformation of polypeptide segments in proteins, Proteins 40, 135–144 (2000)CrossRef C.M. Deane, T.L. Blundell: A novel exhaustive search algorithm for predicting the conformation of polypeptide segments in proteins, Proteins 40, 135–144 (2000)CrossRef
11.48.
Zurück zum Zitat S. Sucha, R.F. Dubose, C.J. March, S. Subashini: Modeling protein loops using a ϕ i+1, ψ i dimer database, Protein Sci. 4, 1412–1420 (1995)CrossRef S. Sucha, R.F. Dubose, C.J. March, S. Subashini: Modeling protein loops using a ϕ i+1, ψ i dimer database, Protein Sci. 4, 1412–1420 (1995)CrossRef
11.49.
Zurück zum Zitat V.Z. Spassov, P.K. Flook, L. Yan: LOOPER: A molecular mechanics-based algorithm for protein loop prediction, Protein Eng. 21, 91–100 (2008)CrossRef V.Z. Spassov, P.K. Flook, L. Yan: LOOPER: A molecular mechanics-based algorithm for protein loop prediction, Protein Eng. 21, 91–100 (2008)CrossRef
11.50.
Zurück zum Zitat A.A. Canutescu, R.L. Dunbrack Jr.: Cyclic coordinate descent: A robotics algorithm for protein loop closure, Protein Sci. 12, 963–972 (2003)CrossRef A.A. Canutescu, R.L. Dunbrack Jr.: Cyclic coordinate descent: A robotics algorithm for protein loop closure, Protein Sci. 12, 963–972 (2003)CrossRef
11.51.
Zurück zum Zitat P.S. Shenkin, D.L. Yarmush, R.M. Fine, H. Wang, C. Levinthal: Predicting antibody hypervariable loop conformation. I. Ensembles of random conformations for ringlike structures, Biopolymers 26, 2053–2085 (1987)CrossRef P.S. Shenkin, D.L. Yarmush, R.M. Fine, H. Wang, C. Levinthal: Predicting antibody hypervariable loop conformation. I. Ensembles of random conformations for ringlike structures, Biopolymers 26, 2053–2085 (1987)CrossRef
11.52.
Zurück zum Zitat J. Lee, D. Lee, H. Park, E.A. Coutsias, C. Seok: Protein loop modeling by using fragment assembly and analytical loop closure, Proteins 78(16), 3428–3436 (2010)CrossRef J. Lee, D. Lee, H. Park, E.A. Coutsias, C. Seok: Protein loop modeling by using fragment assembly and analytical loop closure, Proteins 78(16), 3428–3436 (2010)CrossRef
11.53.
Zurück zum Zitat T. Hurst: Flexible 3D searching: The directed tweak technique, J. Chem. Inf. Comput. Sci. 34, 190–196 (1994)CrossRef T. Hurst: Flexible 3D searching: The directed tweak technique, J. Chem. Inf. Comput. Sci. 34, 190–196 (1994)CrossRef
11.54.
Zurück zum Zitat M.A. DePristo, P.I.W. de Bakker, S.C. Lovell, T.L. Blundell: Ab initio construction of polypeptide fragments: Efficient generation of accurate, representative ensembles, Proteins 51, 41–55 (2003)CrossRef M.A. DePristo, P.I.W. de Bakker, S.C. Lovell, T.L. Blundell: Ab initio construction of polypeptide fragments: Efficient generation of accurate, representative ensembles, Proteins 51, 41–55 (2003)CrossRef
11.55.
Zurück zum Zitat M.P. Jacobson, D.L. Pincus, C.S. Rapp, T.J.F. Day, B. Honig, D.E. Shaw, R.A. Friesner: A hierarchical approach to all-atom protein loop prediction, Proteins 55, 351–367 (2004)CrossRef M.P. Jacobson, D.L. Pincus, C.S. Rapp, T.J.F. Day, B. Honig, D.E. Shaw, R.A. Friesner: A hierarchical approach to all-atom protein loop prediction, Proteins 55, 351–367 (2004)CrossRef
11.56.
Zurück zum Zitat P. Benkert, S.C.E.C. Tosatto, D. Schomburg: QMEAN: A comprehensive scoring function for model quality assessment, Proteins 71(1), 261–277 (2007)CrossRef P. Benkert, S.C.E.C. Tosatto, D. Schomburg: QMEAN: A comprehensive scoring function for model quality assessment, Proteins 71(1), 261–277 (2007)CrossRef
11.57.
Zurück zum Zitat P. Benkert, M. Kunzli, T. Schwede: QMEAN server for protein model quality estimation, Nucleic Acids Res. 37(2), W510–514 (2009)CrossRef P. Benkert, M. Kunzli, T. Schwede: QMEAN server for protein model quality estimation, Nucleic Acids Res. 37(2), W510–514 (2009)CrossRef
11.58.
Zurück zum Zitat S. Kelm, J. Shi, C.M. Deane: MEDELLER: Homology-based coordinate generation for membrane proteins, Bioinformatics 26(22), 2833–2840 (2010)CrossRef S. Kelm, J. Shi, C.M. Deane: MEDELLER: Homology-based coordinate generation for membrane proteins, Bioinformatics 26(22), 2833–2840 (2010)CrossRef
11.59.
Zurück zum Zitat A. Elofsson, G. von Heijne: Membrane protein structure: Prediction versus reality, Annu. Rev. Biochem. 76(1), 125–140 (2007)CrossRef A. Elofsson, G. von Heijne: Membrane protein structure: Prediction versus reality, Annu. Rev. Biochem. 76(1), 125–140 (2007)CrossRef
11.60.
Zurück zum Zitat M. Punta, L.R. Forrest, H. Bigelow, A. Kernytsky, J. Liu, B. Rost: Membrane protein prediction methods, Methods 41(4), 460–474 (2007)CrossRef M. Punta, L.R. Forrest, H. Bigelow, A. Kernytsky, J. Liu, B. Rost: Membrane protein prediction methods, Methods 41(4), 460–474 (2007)CrossRef
11.61.
Zurück zum Zitat M.A. Lomize, A.L. Lomize, I.D. Pogozheva, H.I. Mosberg: OPM: Orientations of proteins in membranes database, Bioinformatics 22(5), 623–625 (2006)CrossRef M.A. Lomize, A.L. Lomize, I.D. Pogozheva, H.I. Mosberg: OPM: Orientations of proteins in membranes database, Bioinformatics 22(5), 623–625 (2006)CrossRef
11.62.
Zurück zum Zitat G.E. Tusnády, Z. Dosztányi, I. Simon: PDB: Selection and membrane localization of transmembrane proteins in the protein data bank, Nucleic Acids Res. 33(1), D275–D278 (2005) G.E. Tusnády, Z. Dosztányi, I. Simon: PDB: Selection and membrane localization of transmembrane proteins in the protein data bank, Nucleic Acids Res. 33(1), D275–D278 (2005)
11.63.
Zurück zum Zitat K.A. Scott, P.J. Bond, A. Ivetac, A.P. Chetwynd, S. Khalid, M.S. Sansom: Coarse-grained MD simulations of membrane protein-bilayer self-assembly, Structure 16(4), 621–630 (2008)CrossRef K.A. Scott, P.J. Bond, A. Ivetac, A.P. Chetwynd, S. Khalid, M.S. Sansom: Coarse-grained MD simulations of membrane protein-bilayer self-assembly, Structure 16(4), 621–630 (2008)CrossRef
11.64.
Zurück zum Zitat S. Kelm, J. Shi, C.M. Deane: iMembrane: Homology-based membrane-insertion of proteins, Bioinformatics 25(8), 1086–1088 (2009)CrossRef S. Kelm, J. Shi, C.M. Deane: iMembrane: Homology-based membrane-insertion of proteins, Bioinformatics 25(8), 1086–1088 (2009)CrossRef
11.65.
Zurück zum Zitat L. Forrest, C. Tang, B. Honig: On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins, Biophys. J. 91(2), 508–517 (2006)CrossRef L. Forrest, C. Tang, B. Honig: On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins, Biophys. J. 91(2), 508–517 (2006)CrossRef
Metadaten
Titel
Protein Modeling and Structural Prediction
verfasst von
Sebastian Kelm
Yoonjoo Choi
Charlotte M. Deane
Copyright-Jahr
2014
DOI
https://doi.org/10.1007/978-3-642-30574-0_11