Effective protein model structure refinement by loop modeling and overall relaxation

Proteins: Structure, Function and Bioinformatics

Volumn 84, Issue S1, 2016, Pages 293-301

  Lee, Gyu Rie ^a   Heo, Lim ^a   Seok, Chaok ^a  

^a Seoul National University   (South Korea)

Author keywords

ANM; CASP; loop modeling; MD relaxation; refinement; scoring function

Indexed keywords

PROTEIN;

ALGORITHM; ALPHA HELIX; BETA SHEET; BIOLOGY; CHEMISTRY; COMPUTER SIMULATION; HUMAN; INTERNET; MOLECULAR MODEL; PROCEDURES; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN MOTIF; PROTEIN TERTIARY STRUCTURE; SEQUENCE HOMOLOGY; SOFTWARE; STATISTICAL MODEL; STATISTICS AND NUMERICAL DATA; THERMODYNAMICS;

ALGORITHMS; AMINO ACID MOTIFS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; HUMANS; INTERNET; MODELS, MOLECULAR; MODELS, STATISTICAL; PROTEIN CONFORMATION, ALPHA-HELICAL; PROTEIN CONFORMATION, BETA-STRAND; PROTEIN FOLDING; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE; THERMODYNAMICS;

EID: 84937469123     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24858     Document Type: Article

References (45)

1. Zhang Y. Protein structure prediction: when is it useful? Curr Opin Struct Biol 2009; 19:145–155.
2. Cavasotto CN, Phatak SS. Homology modeling in drug discovery: current trends and applications. Drug Discov Today 2009; 14:676–683.
3. Giorgetti A, Raimondo D, Miele AE, Tramontano A. Evaluating the usefulness of protein structure models for molecular replacement. Bioinformatics 2005; 21(Suppl 2):ii72–76.
4. Martí-Renom MA, Stuart AC, Fiser A, Sánchez R, Melo F, Sali A. Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 2000; 29:291–325.
5. Baker D, Sali A. Protein structure prediction and structural genomics. Science 2001; 294:93–96.
6. Zhang Y. Progress and challenges in protein structure prediction. Curr Opin Struct Biol 2008; 18:342–348.
7. Lee MR, Tsai J, Baker D, Kollman PA. Molecular dynamics in the endgame of protein structure prediction. J Mol Biol 2001; 313:417–430.
8. Chen JH, Brooks CL. Can molecular dynamics simulations provide high-resolution refinement of protein structure? Proteins 2007; 67:922–930.
9. Ishitani R, Terada T, Shimizu K. Refinement of comparative models of protein structure by using multicanonical molecular dynamics simulations. Mol Simulat 2008; 34:327–336.
10. Raval A, Piana S, Eastwood MP, Dror RO, Shaw DE. Refinement of protein structure homology models via long, all-atom molecular dynamics simulations. Proteins 2012; 80:2071–2079.
11. Mirjalili V, Feig M. Protein structure refinement through structure selection and averaging from molecular dynamics ensembles. J Chem Theory Comput 2013; 9:1294–1303.
12. Mirjalili V, Noyes K, Feig M. Physics-based protein structure refinement through multiple molecular dynamics trajectories and structure averaging. Proteins 2014; 82:196–207.
13. Chopra G, Summa CM, Levitt M. Solvent dramatically affects protein structure refinement. Proc Natl Acad Sci U S A 2008; 105:20239–20244.
14. Fan H, Mark AE. Refinement of homology-based protein structures by molecular dynamics simulation techniques. Protein Sci 2004; 13:211–220.
15. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules (1995, 117, 5179-5197). J Am Chem Soc 1996; 118:2309–2309.
16. Best RB, Zhu X, Shim J, Lopes PEM, Mittal J, Feig M, MacKerell AD. Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles. J Chem Theory Comput 2012; 8:3257–3273.
17. Jorgensen WL, Maxwell DS, Tirado-Rives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 1996; 118:11225–11236.
18. Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B 2001; 105:6474–6487.
19. Gront D, Kmiecik S, Blaszczyk M, Ekonomiuk D, Koliński A. Optimization of protein models. Wires Comput Mol Sci 2012; 2:479–493.
20. Zhou H, Zhou Y. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci 2002; 11:2714–2726.
21. Zhu J, Xie L, Honig B. Structural refinement of protein segments containing secondary structure elements: Local sampling, knowledge-based potentials, and clustering. Proteins 2006; 65:463–479.
22. Zhu J, Fan H, Periole X, Honig B, Mark AE. Refining homology models by combining replica-exchange molecular dynamics and statistical potentials. Proteins 2008; 72:1171–1188.
23. Yang Y, Zhou Y. Specific interactions for ab initio folding of protein terminal regions with secondary structures. Proteins 2008; 72:793–803.
24. Summa CM, Levitt M. Near-native structure refinement using in vacuo energy minimization. Proc Natl Acad Sci U S A 2007; 104:3177–3182.
25. Samudrala R, Moult J. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol 1998; 275:895–916.
26. Rodrigues JP, Levitt M Chopra G. KoBaMIN: a knowledge-based minimization web server for protein structure refinement. Nucleic Acids Res 2012; 40:W323–W328.
27. Kortemme T, Morozov AV, Baker D. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J Mol Biol 2003; 326:1239–1259.
28. Heo L, Park H, Seok C. GalaxyRefine: protein structure refinement driven by side-chain repacking. Nucleic Acids Res 2013; 41:W384–388.
29. Jagielska A, Wroblewska L, Skolnick J. Protein model refinement using an optimized physics-based all-atom force field. Proc Natl Acad Sci U S A 2008; 105:8268–8273.
30. Zhang J, Liang Y, Zhang Y. Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling. Structure 2011; 19:1784–1795.
31. Nugent T, Cozzetto D, Jones DT. Evaluation of predictions in the CASP10 model refinement category. Proteins 2014; 82(Suppl 2):98–111.
32. Krivov GG, Shapovalov MV, Dunbrack RL, Jr. Improved prediction of protein side-chain conformations with SCWRL4. Proteins 2009; 77:778–795.
33. Bakan A, Meireles LM, Bahar I. ProDy: protein dynamics inferred from theory and experiments. Bioinformatics 2011; 27:1575–1577.
34. Tirion MM. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys Rev Lett 1996; 77:1905–1908.
35. Wallner B, Elofsson A. Pcons5: combining consensus, structural evaluation and fold recognition scores. Bioinformatics 2005; 21:4248–4254.
36. Xiang Z, Soto CS, Honig B. Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction. Proc Natl Acad Sci U S A 2002; 99:7432–7437.
37. Park H, Lee GR, Heo L, Seok C. Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments. PLoS One 2014; 9:e113811
38. Lee J, Lee D, Park H, Coutsias EA, Seok C. Protein loop modeling by using fragment assembly and analytical loop closure. Proteins 2010; 78:3428–3436.
39. Coutsias EA, Seok C, Jacobson MP, Dill KA. A kinematic view of loop closure. J Comput Chem 2004; 25:510–528.
40. Lee J, Scheraga HA, Rackovsky S. New optimization method for conformational energy calculations on polypeptides: Conformational space annealing. J Comput Chem 1997; 18:1222–1232.
41. Kopp J, Bordoli L, Battey JND, Kiefer F, Schwede T. Assessment of CASP7 predictions for template-based modeling targets. Proteins 2007; 69:38–56.
42. Kryshtafovych A, Monastyrskyy B, Fidelis K. CASP prediction center infrastructure and evaluation measures in CASP10 and CASP ROLL. Proteins 2014; 82(Suppl 2):7–13.
43. Chen VB, Arendall WB, III, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 2010; 66:12–21.
44. Park H, Seok C. Refinement of unreliable local regions in template-based protein models. Proteins 2012; 80:1974–1986.
45. Park H, Ko J, Joo K, Lee J, Seok C, Lee J. Refinement of protein termini in template-based modeling using conformational space annealing. Proteins 2011; 79:2725–2734.