Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Potapov, Vladimir ^a   Cohen, Mati ^a   Inbar, Yuval ^a   Schreiber, Gideon ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

ATTAINABLE ACCURACY; COMPUTATIONAL STRUCTURE; HOMOLOGY MODELLING; INTERACTION GEOMETRIES; INTERACTIVE EXPLORATION; PROTEIN STRUCTURES; PROTEIN-PROTEIN DOCKING; SIDE-CHAIN INTERACTIONS;

CHAINS; COMPUTATIONAL GEOMETRY; KNOWLEDGE BASED SYSTEMS;

PROTEINS;

CASPASE 7; CASPASE 8; PROTEIN;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; PROTEIN CONFORMATION; PROTEIN FOLDING; STRUCTURAL HOMOLOGY;

CASPASE 7; CASPASE 8; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 77954402860     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-374     Document Type: Article

References (51)

1. Lazaridis T, Karplus M. Effective energy functions for protein structure prediction. Curr Opin Struct Biol 2000, 10:139-145. 10.1016/S0959-440X(00)00063-4, 10753811.
2. Brooks B, Bruccoleri R, Olafson B, States D, Swaminathan S, Karplus M. CHARMM - A program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983, 4:187-217.
3. Pearlman D, Case D, Caldwell J, Ross W, Cheatham T, Debolt S, Ferguson D, Seibel G, Kollman P. AMBER, a package of computer-programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules. Comput Phys Commun 1995, 91:1-41.
4. Pokala N, Handel TM. Energy functions for protein design: adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity. J Mol Biol 2005, 347:203-227. 10.1016/j.jmb.2004.12.019, 15733929.
5. Poole AM, Ranganathan R. Knowledge-based potentials in protein design. Curr Opin Struct Biol 2006, 16:508-513. 10.1016/j.sbi.2006.06.013, 16843652.
6. Summa CM, Levitt M. Near-native structure refinement using in vacuo energy minimization. Proc Natl Acad Sci USA 2007, 104:3177-3182. 10.1073/pnas.0611593104, 1802011, 17360625.
7. Finkelstein AV, AYa B, Gutin AM. Why do protein architectures have Boltzmann-like statistics?. Proteins 1995, 23:142-150. 10.1002/prot.340230204, 8592696.
8. Ben-Naim A. Statistical potentials extracted from protein structures: Are these meaningful potentials?. J Chem Phys 1997, 107:3698-3706.
9. Skolnick J, Jaroszewski L, Kolinski A, Godzik A. Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct?. Protein Sci 1997, 6:676-688. 10.1002/pro.5560060317, 2143667, 9070450.
10. Furuichi E, Koehl P. Influence of protein structure databases on the predictive power of statistical pair potentials. Proteins 1998, 31:139-149. 10.1002/(SICI)1097-0134(19980501)31:2<139::AID-PROT4>3.0.CO;2-H, 9593188.
11. Thomas PD, Dill KA. Statistical potentials extracted from protein structures: how accurate are they?. J Mol Biol 1996, 257:457-469. 10.1006/jmbi.1996.0175, 8609636.
12. Buchete NV, Straub JE, Thirumalai D. Development of novel statistical potentials for protein fold recognition. Curr Opin Struct Biol 2004, 14:225-232. 10.1016/j.sbi.2004.03.002, 15093838.
13. MacArthur MW, Driscoll PC, Thornton JM. NMR and crystallography--complementary approaches to structure determination. Trends Biotechnol 1994, 12:149-153. 10.1016/0167-7799(94)90074-4, 7764895.
14. Sippl MJ. Recognition of errors in three-dimensional structures of proteins. Proteins 1993, 17:355-362. 10.1002/prot.340170404, 8108378.
15. Bowie JU, Luthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 1991, 253:164-170. 10.1126/science.1853201, 1853201.
16. Chiu TL, Goldstein RA. How to generate improved potentials for protein tertiary structure prediction: a lattice model study. Proteins 2000, 41:157-163. 10.1002/1097-0134(20001101)41:2<157::AID-PROT10>3.0.CO;2-W, 10966569.
17. Lu M, Dousis AD, Ma J. OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing. J Mol Biol 2008, 376:288-301. 10.1016/j.jmb.2007.11.033, 2669442, 18177896.
18. Samudrala R, Moult J. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol 1998, 275:895-916. 10.1006/jmbi.1997.1479, 9480776.
19. 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. 10.1110/ps.0217002, 2373736, 12381853.
20. Bahar I, Jernigan RL. Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J Mol Biol 1997, 266:195-214. 10.1006/jmbi.1996.0758, 9054980.
21. Kolinski A, Jaroszewski L, Rotkiewicz P, Skolnick J. An efficient Monte Carlo model of protein chains. Modeling the short-range correlations between side group centers of mass. J Phys Chem B 1998, 102:4628-4637.
22. Lu H, Skolnick J. A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins 2001, 44:223-232. 10.1002/prot.1087, 11455595.
23. Buchete NV, Straub JE, Thirumalai D. Orientational potentials extracted from protein structures improve native fold recognition. Protein Sci 2004, 13:862-874. 10.1110/ps.03488704, 2280067, 15044723.
24. Miyazawa S, Jernigan RL. How effective for fold recognition is a potential of mean force that includes relative orientations between contacting residues in proteins?. J Chem Phys 2005, 122:024901. 10.1063/1.1824012, 15638624.
25. Misura KM, Morozov AV, Baker D. Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction. J Mol Biol 2004, 342:651-664. 10.1016/j.jmb.2004.07.038, 15327962.
26. Lu M, Dousis AD, Ma J. OPUS-Rota: a fast and accurate method for side-chain modeling. Protein Sci 2008, 17:1576-1585. 10.1110/ps.035022.108, 2525522, 18556476.
27. Cohen M, Potapov V, Schreiber G. Four distances between pairs of amino acids provide a precise description of their interaction. PLoS Comput Biol 2009, 5:e1000470. 10.1371/journal.pcbi.1000470, 2715887, 19680437.
28. Lazaridis T, Karplus M. Effective energy function for proteins in solution. Proteins 1999, 35:133-152. 10.1002/(SICI)1097-0134(19990501)35:2<133::AID-PROT1>3.0.CO;2-N, 10223287.
29. Eisenberg D, McLachlan AD. Solvation energy in protein folding and binding. Nature 1986, 319:199-203. 10.1038/319199a0, 3945310.
30. Wesson L, Eisenberg D. Atomic solvation parameters applied to molecular dynamics of proteins in solution. Protein Sci 1992, 1:227-235. 10.1002/pro.5560010204, 2142195, 1304905.
31. Samudrala R, Levitt M. Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction. Protein Sci 2000, 9:1399-1401. 10.1110/ps.9.7.1399, 2144680, 10933507.
32. Shen MY, Sali A. Statistical potential for assessment and prediction of protein structures. Protein Sci 2006, 15:2507-2524. 10.1110/ps.062416606, 2242414, 17075131.
33. Rajgaria R, McAllister SR, Floudas CA. A novel high resolution Calpha--Calpha distance dependent force field based on a high quality decoy set. Proteins 2006, 65:726-741. 10.1002/prot.21149, 16981202.
34. Voigt CA, Gordon DB, Mayo SL. Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design. J Mol Biol 2000, 299:789-803. 10.1006/jmbi.2000.3758, 10835284.
35. Word JM, Lovell SC, LaBean TH, Taylor HC, Zalis ME, Presley BK, Richardson JS, Richardson DC. Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. J Mol Biol 1999, 285:1711-1733. 10.1006/jmbi.1998.2400, 9917407.
36. Cohen M, Reichmann D, Neuvirth H, Schreiber G. Similar chemistry, but different bond preferences in inter versus intra-protein interactions. Proteins 2008, 72:741-753. 10.1002/prot.21960, 18260101.
37. Neuvirth H, Raz R, Schreiber G. ProMate: a structure based prediction program to identify the location of protein-protein binding sites. J Mol Biol 2004, 338:181-199. 10.1016/j.jmb.2004.02.040, 15050833.
38. Baker D, Sali A. Protein structure prediction and structural genomics. Science 2001, 294:93-96. 10.1126/science.1065659, 11588250.
39. Read RJ, Chavali G. Assessment of CASP7 predictions in the high accuracy template-based modeling category. Proteins 2007, 69(Suppl 8):27-37. 10.1002/prot.21662, 17894351.
40. Singh J, Thornton JM. Atlas of protein side-chain interactions. 1992, Oxford; New York: IRL Press at Oxford University Press.
41. Desmet J, Demaeyer M, Hazes B, Lasters I. The dead-end elimination theorem and its use in protein side-cahin positioning. Nature 1992, 356:539-542.
42. Eyal E, Gerzon S, Potapov V, Edelman M, Sobolev V. The limit of accuracy of protein modeling: influence of crystal packing on protein structure. J Mol Biol 2005, 351:431-442. 10.1016/j.jmb.2005.05.066, 16005885.
43. Potapov V, Cohen M, Schreiber G. Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details. Protein Eng Des Sel 2009,
44. Wang G, Dunbrack RL. PISCES: a protein sequence culling server. Bioinformatics 2003, 19:1589-1591. 10.1093/bioinformatics/btg224, 12912846.
45. Dunbrack RL, Cohen FE. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci 1997, 6:1661-1681. 10.1002/pro.5560060807, 2143774, 9260279.
46. Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D. Design of a novel globular protein fold with atomic-level accuracy. Science 2003, 302:1364-1368. 10.1126/science.1089427, 14631033.
47. Neria E, Fischer S, Karplus M. Simulation of activation free energies in molecular systems. J Chem Phys 1996, 105:1902-1921.
48. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000, 28:235-242. 10.1093/nar/28.1.235, 102472, 10592235.
49. Tress M, Ezkurdia I, Graña O, López G, Valencia A. Assessment of predictions submitted for the CASP6 comparative modeling category. Proteins 2005, 61(Suppl 7):27-45. 10.1002/prot.20720, 16187345.
50. Xiang Z, Honig B. Extending the accuracy limits of prediction for side-chain conformations. J Mol Biol 2001, 311:421-430. 10.1006/jmbi.2001.4865, 11478870.
51. Krivov GG, Shapovalov MV, Dunbrack RLJ. Improved prediction of protein side-chain conformations with SCWRL4. Proteins 2009, 77:778-795. 10.1002/prot.22488, 19603484.