Capturing native/native like structures with a physico-chemical metric (pcSM) in protein folding

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1834, Issue 8, 2013, Pages 1520-1531

  Mishra, Avinash ^a   Rao, Satyanarayan ^a   Mittal, Aditya ^a   Jayaram, B ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY DELHI   (India)

Author keywords

Decoy; Native structure; Protein folding; Protein structure prediction; Scoring function

Indexed keywords

PROTEIN; CASP5 PROTEIN, HUMAN; CASP9 PROTEIN, HUMAN; CASPASE; CASPASE 9;

ACCURACY; ALGORITHM; ARTICLE; BIOMETRY; COMPUTER MODEL; CONTROLLED STUDY; ENERGY; MOLECULAR DYNAMICS; PARAMETERS; PHYSICAL CHEMISTRY; PHYSICOCHEMICAL METRIC; PREDICTION; PRIORITY JOURNAL; PROPENSITY SCORE; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; SCORING SYSTEM; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; COMPUTER SIMULATION; HUMAN;

ALGORITHMS; CASPASE 9; CASPASES; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; HUMANS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; SOFTWARE;

EID: 84882263302     PISSN: 15709639     EISSN: 18781454     Source Type: Journal    
DOI: 10.1016/j.bbapap.2013.04.023     Document Type: Article

References (140)

1. S. Salzberg, D. Searls, S. Kasif, Grand challenges in computational biology, Computational Methods in Molecular Biology, Elsevier Science, 1998.
2. R. Unger, J. Moult, Bull. Math. Biol. 55 (1993) 1183-1198.
3. A.S. Fraenkel, Bull. Math. Biol. 55 (1993) 1199-1210.
4. L Pauling, R.B. Corey, H.R. Branson, The structure of proteins: two hydrogen-bonded helical configurations of the polypeptide chain, Proc. Natl. Acad. Sci. U. S. A. 37 (1951) 205-211.
5. L Pauling, R.B. Corey, The pleated sheet, a new layer configuration of polypeptide chains, Proc. Natl. Acad. Sci. U. S. A. 37 (1951) 251-256.
6. L Pauling, R.B. Corey, Atomic coordinates and structure factors for two helical configurations of polypeptide chains, Proc. Natl. Acad. Sci. U. S. A. 37 (1951) 235-240.
7. P.Y. Chou, G.D. Fasman, Prediction of protein conformation, Biochemistry 13 (1974) 222-245.
8. T.Z. Sen, R.L. Jernigan, J. Garnier, A. Kloczkowski, GOR V server for protein secondary structure prediction, Bioinformatics 21 (2005) 2787-2788. (Pubitemid 40852330)
9. V.I. Lim, Structural principles of the globular organization of protein chains, a stereochemical theory of globular protein secondary structure, J. Mol. Biol. 88 (1974) 857-872.
10. W. Kabsch, C. Sander, Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features, Biopolymers 22 (1983) 2577-2637.
11. W. Kabsch, C. Sander, How good are predictions of protein secondary structure? FEBS Lett 155 (1983) 179-182.
12. B. Rost, C. Sander, Prediction of protein secondary structure at better than 70% accuracy, J. Mol. Biol. 232 (1993) 584-599. (Pubitemid 23251181)
13. M.J. Zvelebil, Prediction of protein secondary structure and active sites using the alignment of homologous sequences, J. Mol. Biol. 195 (1987) 957-961.
14. A.A. Salamov, V.V. Solovyev, Protein secondary structure prediction using local alignments, J. Mol. Biol. 268 (1997) 31-36. (Pubitemid 27192676)
15. P.K. Mehta, A simple and fast approach to prediction of protein secondary structure from multiply aligned sequences with accuracy above 70%, Protein Sci. 4 (1995) 2517-2525.
16. C. Geourjon, G. Deleage, SOPM: a self-optimized method for protein secondary structure prediction, Protein Eng. 7 (1994) 157-164. (Pubitemid 24031206)
17. D.T. Jones, Protein secondary structure prediction based on position-specific scoring matrices, J. Mol. Biol. 292 (1999) 195-202. (Pubitemid 29435759)
18. C. Cole, J.D. Barber, The Jpred 3 secondary structure prediction server, Nucleic Acids Res. 36 (2008) W197-W201.
19. H. Frauenfelder, S. Sligar, P.G. Wolynes, The energy landscapes and motions of proteins, Science 254 (1991) 1598-1603. (Pubitemid 21917496)
20. J.D. Bryngelson, J.N. Onuchic, N.D. Socci, P.G. Wolynes, Funnels, pathways, and the energy landscape of protein folding: a synthesis, Proteins 21 (1995) 167-195.
21. C.B. Anfinsen, Principles that govern the folding of protein chains, Science 181 (1973) 223-230.
22. K.A. Dill, H.S. Chan, From Levinthal to pathways to funnels, Nat. Struct Biol. 4 (1997) 10-19. (Pubitemid 27020916)
23. K.A. Dill, S.B. Ozkan, T.R. Weikl, J.D. Chodera, V.A. Voelz, The protein folding problem: when will it be solved? Curr. Opin. Struct. Biol. 17 (2007) 342-346. (Pubitemid 47021366)
24. P. Kollman, Free energy calculations: applications to chemical and biochemical phenomena, Chem. Rev. 93 (1993) 2395-2417.
25. W. Jorgensen, Free energy calculations: a breakthrough for modeling organic chemistry in solution, Acc. Chem. Res. 22 (1989) 184-189.
26. W.F. Van Gunsteren, H.J.C. Berendsen, Computer simulation of molecular dynamics: methodology, applications and perspectives in chemistry, Angew. Chem. Int Ed Engl. 29 (1990) 992-1023.
27. D.L. Beveridge, F.M. DiCapua, Free energy via molecular simulation: applications to chemical and biomolecular systems, Annu. Rev. Biophys. Biomol. Struct. 18 (1989) 431-492.
28. B. Jayaram, D. Sprous, D.L. Beveridge, Solvation free energy of biomacromolecules: parameters for a modified generalized born model consistent with the AMBER force field, J. Phys. Chem. B 102 (1998) 9571-9576. (Pubitemid 128611876)
29. P. Kalra, T.V. Reddy, B. Jayaram, Free energy component analysis for drug design: a case study of HIV-1 protease-inhibitor binding, J. Med. Chem. 44 (2001) 4325-4338. (Pubitemid 33131659)
30. B. Jayaram, D. Sprous, M.A. Young, D.L. Beveridge, Free energy analysis of the conformational preferences of A and B forms of DNA in solution, J. Am. Chem. Soc. 120 (1998) 10629-10633. (Pubitemid 28498806)
31. P. Narang, K. Bhushan, S. Bose, B. Jayaram, A computational pathway for bracketing native-like structures for small alpha helical globular proteins, Phys. Chem. Chem. Phys. 7 (2005) 2364-2375. (Pubitemid 40855584)
32. J. Pillardy, C. Czaplewski, A. Liwo, W.J. Wedemeyer, J. Lee, D.R. Ripoll, P. Arlukowicz, S. Oldziej, Y.A. Arnautova, H.A. Scheraga, Development of physics-based energy functions that predict medium-resolution structures for protein of the á, â and á/â structural classes, J. Phys. Chem. B 105 (2001) 7299-7311. (Pubitemid 35338954)
33. K.A. Dill, Dominant forces in protein folding, Biochemistry 29 (31) (1990) 7133-7155. (Pubitemid 20230041)
34. B.N. Dominy, E.I. Shakhnovich, Native atom types for knowledge-based potentials: application to binding energy prediction, J. Med. Chem. 47 (2004) 4538-4558. (Pubitemid 39096841)
35. J. Shimada, A.I. Ischenko, E.I. Shakhnovich, Analysis of knowledge-based protein-ligand potentials using a self-consistent method, Protein Sci. 9 (2000) 765-775. (Pubitemid 30217626)
36. T. Lazaridis, M. Karplus, Effective energy functions for protein structure prediction, Curr. Opin. Struct. Biol. 10 (2000) 139-145. (Pubitemid 30198938)
37. M.J. Sippl, Knowledge-based potentials for proteins, Curr. Opin. Struct. Biol. 5 (1995) 229-235.
38. H. Lu, J. Skolnick, A distance-dependent atomic knowledge-based potential for improved protein structure selection, Proteins: Struct. Funct. Genet. 44 (2001) 223-232. (Pubitemid 32702231)
39. R.L. Jernigan, I. Bahar, Structure derived potential and protein simulation, Curr. Opin. Struct. Biol. 6 (1996) 195-209.
40. D. Mohanty, B.N. Dominy, A. Kolinski, C.L. Brooks III, J. Skolnick, Correlation between knowledge-based and detailed atomic potentials: application to the unfolding of the GCN4 leucine zipper, Proteins: Struct. Funct. Genet. 35 (1999) 447-452. (Pubitemid 29264841)
41. L. Thukral, S.R. Shenoy, K. Bhusan, B. Jayaram, ProRegIn: a regularity index for the selection of native-like tertiary structures of proteins, J. Biosci. 32 (1) (2007) 71-81. (Pubitemid 46465758)
42. P.W. Rose, The RCSB Protein Data Bank: redesigned web site and web services, Nucleic Acids Res. 39 (2011) D392-D401.
43. O. Lund, M. Nielsen, C. Lundegard, P. Worning, CPHmodels 2.0: X3M a computer program to extract 3dmodels, Abstract at the CASP5 Conference, 2002, p. A102.
44. N. Guex, M.C. Peitsch, SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling, Electrophoresis 18 (1997) 2714-2723. (Pubitemid 28059943)
45. C. Lambert, N. Leonard, X. De Bolle, E. Depiereux, ESyPred3D: prediction of proteins 3D structures, Bioinformatics 18 (2002) 1250-1256.
46. A. Sali, T. Blundell, Comparative protein modeling by satisfaction of spatial restraints, J. Mol. Biol. 234 (1993) 779-815. (Pubitemid 24007801)
47. C. Combat, M. Jambon, G. Deleage, C. Geourjon, Geno3D: automatic comparative molecular modelling of protein, Bioinformatics 18 (2002) 213-214. (Pubitemid 34145058)
48. P.A. Bates, L.A. Kelley, R.M. MacCallum, M. Sternberg, Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM, Proteins 45 (2001) 39-46. (Pubitemid 34113166)
49. B. Contreras-Moreira, P.A. Bates, Domain fishing: a first step in protein comparative modeling, Bioinformatics 18 (2002) 1141-1142. (Pubitemid 34919239)
50. A. Lobley, M.I. Sadowski, D.T. Jones, pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination, Bioinformatics 25 (2009) 1761-1767.
51. L. Jaroszewski, L. Rychlewski, Z. Li, W. Li, A. Godzik, FFAS03: a server for profile-profile sequence alignments, Nucleic Acids Res. 33 (2005) W284-W288. (Pubitemid 44529927)
52. L.A. Kelley, M.J. Sternberg, Protein structure prediction on the Web: a case study using the Phyre server, Nat. Protoc. 4 (2009) 363-371.
53. H. Zhou, S.B. Pandit, J. Skolnick, Performance of the Pro-sp3-TASSER server in CASP8, Proteins 77 (Suppl. 9) (2009) S123-S127.
54. H. Chen, J. Skolnick, M-TASSER: an algorithm for protein quaternary structure prediction, Biophys. J. 94 (2008) 918-928. (Pubitemid 351162458)
55. W. Zhang, S. Liu, Y. Zhou, SP5: improving protein fold recognition by using torsion angle profiles and profile-based gap penalty model, PLoS One 3 (2008) e2325.
56. N. Fernandez-Fuentes, J.M. Dybas, A. Fiser, Structural characteristics of novel protein folds, PLoS Comput. Biol. 6 (4) (2010).
57. J. Cheng, A.Z. Randell, M.J. Sweredoski, P. Baldi, SCRATCH: a protein structure and structural feature, Nucleic Acids Res. 33 (2005) W72-W76. (Pubitemid 44529882)
58. B. Jayaram, K. Bhushan, S.R. Shenoy, P. Narang, S. Bose, P. Agrawal, D. Sahu, V. Pandey, Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins, Nucleic Acids Res. 34 (2006) 6195-6204. (Pubitemid 44942740)
59. L.H. Hung, S.C. Ngan, T. Liu, R. Samudrala, PROTINFO: new algorithms for enhanced protein structure prediction, Nucleic Acids Res. 33 (2005) W77-W80. (Pubitemid 44529883)
60. C.A. Rohl, C.E. Strauss, K.M. Misura, D. Baker, Protein structure prediction using Rosetta, Meth. Enzymol. 383 (2004) 66-93. (Pubitemid 38401787)
61. D.E. Kim, D. Chivian, D. Baker, Protein structure prediction and analysis using the Robetta server, Nucleic Acids Res. 32 (2004) W526-W531. (Pubitemid 38997389)
62. T. Ishida, K. Kinoshita, PrDOS: prediction of disordered protein regions from amino acid sequence, Nucleic Acids Res. 35 (2007), (Web Server issue).
63. J.A. McCammon, B.R. Gelin, M. Karplus, Dynamics of folded proteins, Nature 267 (1977) 585-590.
64. A. Li, V. Daggett, Investigation of the solution structure of chymotrypsin inhibitor 2 using molecular dynamics: comparison to X-ray crystallographic and NMR data, Protein Eng. 8 (1995) 1117-1128. (Pubitemid 26066518)
65. V. Daggett, M. Levitt, Molecular dynamics simulation of the molten globule state, Proc. Natl. Acad. Sci. U. S. A. 89 (1992) 5142-5146.
66. M. Levitt, Molecular dynamics of native protein: I. Computer simulation of trajectories, J. Mol. Biol. 168 (1983) 595-620.
67. M. Levitt, Molecular dynamics of native protein. II. Analysis and nature of motion, J. Mol. Biol. 168 (1983) 621-657.
68. J. Tirado-Rives, W.L. Jorgensen, Molecular dynamics simulations of the unfolding of apomyoglobinin water, Biochemistry 32 (1993) 4175-4184. (Pubitemid 23137722)
69. E.M. Boczko, C.L. Brooks III, First principles calculation of the free energy surface for folding of a three helix bundle protein, Science 269 (1995) 393-396.
70. E. Demchuk, D. Bashford, D.A. Case, Dynamics of a type VI reverses turn in a linear peptide in aqueous solution, Fold. Des. 2 (1997) 35-46. (Pubitemid 127740449)
71. X. Daura, B. Jaun, D. Seebach, W.F. van Gunsteren, A.E. Mark, Reversible peptide folding in solution by molecular dynamics simulation, J. Mol. Biol. 280 (1998) 925-932. (Pubitemid 28345025)
72. Y. Duan, P.A. Kollman, Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution, Science 282 (1998) 740-744. (Pubitemid 28489385)
73. U. Mayor, C.M. Johnson, V. Daggett, A.R. Fersht, Protein folding and unfolding in microsecond to nanoseconds by experiment and simulation, Proc. Natl. Acad. Sci. U. S. A. 97 (2000) 13518-13522.
74. B. Zagrovic, E.J. Sorin, V.S. Pande, Beta-hairpin folding simulations in atomistic detail using an implicit solvent model, J. Mol. Biol. 313 (2001) 151-169. (Pubitemid 33001172)
75. C. Simmerling, B. Strockbine, A.E. Roitberg, All-atom structure prediction and folding simulations of a stable protein, J. Am. Chem. Soc. U. S. A. 124 (2002) 11258-11259.
76. C.D. Snow, B. Zagrovic, V.S. Pande, The Trp cage: folding kinetics and unfolded state topology via molecular dynamics simulations, J. Am. Chem. Soc. 124 (2002) 14548-14549. (Pubitemid 35425023)
77. P.L. Freddolino, F. Liu, M. Gruebele, K. Schulten, Ten-microsecond. MD simulation of a fast-folding WW domain, Biophys. J. 94 (2008) 75-77.
78. P.L. Freddolino, S. Park, B. Roux, K. Schulten, Force field bias in protein folding simulations, Biophys. J. 96 (2009) 3772-3780.
79. V.A. Voelz, G.R. Bowman, K. Beauchamp, V.S. Pande, Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39), J. Am. Chem. Soc. 132 (2010) 1526-1528.
80. D.E. Shaw, P. Maragakis, K. Lindorff-Larsen, S. Piana, R.O. Dror, M.P. Eastwood, J.A. Bank, J.M. Jumper, J.K. Salmon, Y. Shan, W. Wriggers, Atomic-level characterization of the structural dynamics of proteins, Science 330 (2010) 341-346.
81. K.A. Dill, S. Banu Ozkan, M. Scott Shell, R. Weikl Thomas, The protein folding problem, Annu. Rev. Biophys. 37 (2008) 289-316.
82. S. Cooper, F. Khatib, A. Treuille, J. Barbero, J. Lee, M. Beenen, A. Leaver-Fay, D. Baker, Z. Popović, Foldit players, Predicting protein structures with a multiplayer online game, Nature 466 (2010) 756-770.
83. J. Moult, K. Fidelis, A. Kryshtafovych, C. Venclovas, Progress over the first decade of CASP experiments, Proteins: Struct. Funct. Bioinform. 7 (2005) 225-236. (Pubitemid 43069977)
84. J.C. Wootton, Non-globular domains in protein sequences: automated segmentation using complexity measures, Comput. Chem. 18 (1994) 269-285.
85. P.J. Flory, Principles of Polymer Chemistry, Cornell University, 1953. 428-429.
86. C. Venclovas, A. Zemla, K. Fidelis, J. Moult, Assessment of progress over the CASP experiments, Proteins 53 (Suppl. 6) (2003) 585-595. (Pubitemid 37352220)
87. A. Fiser, R.K. Do, A. Sali, Modeling of loops in protein structures, Protein Sci. 9 (2000) 1753-1773.
88. A. Kryshtafovych, C. Venclovas, K. Fidelis, J. Moult, Progress over first decade of CASP experiments, Proteins 61 (2005) 225-236. (Pubitemid 43069977)
89. A. Mittal, B. Jayaram, S.R. Shenoy, T.S. Bawa, A Stoichiometry driven universal spatial organization of backbones of folded proteins: are there Chargaff's rules for protein folding? J. Biomol. Struct. Dyn. 28 (2) (2010) 133-142.
90. V. Soundararajan, R. Raman, S. Raguram, V. Sasisekharan, R. Sasisekharan, Atomic interaction networks in the core of protein domains and their native folds, PLoS One 5 (2) (2010) e9391, http://dx.doi.org/10.1371/journal.pone. 0009391.
91. A. Mittal, B. Jayaram, Backbones of folded proteins reveal novel invariant amino-acid neighborhoods, J. Biomol. Struc. Dyn. 28 (4) (2011) 443-454.
92. J. Janin, Surface and inside volume in globular protein, Nature 277 (1979) 491-492.
93. C.C. Palliser, D.A.D. Parry, Quantitative comparison of the ability of hydropathy scales to recognize surface β-strands in proteins, Proteins 42 (2001) 243-255. (Pubitemid 32047333)
94. R.P. Bahdur, P. Chakrabarti, Discriminating the native structure from decoys using scoring functions based on the residue packing in globular proteins, BMC Bioinform. 9 (2009) 76.
95. J. Chen, W.E. Stites, Packing is a key selection factor in the evolution of protein hydrophobic cores, Biochemistry 40 (2001) 5280-15289.
96. R. Wolfenden, L. Anderson, P.M. Cullis, C.C. Southgate, Affinities of amino acid side chains for solvent water, Biochemistry 20 (1981) 849-855.
97. S.B. Dixit, R. Bhasin, E. Rajasekaran, B. Jayaram, Solvation thermodynamics of amino acids: assessment of the electrostatic contribution and force-field dependence, J. Chem. Soc., Faraday Trans. 93 (6) (1997) 1105-1113. (Pubitemid 127820845)
98. J. Kyte, R.F. Doolittle, A simple method for displaying the hydropathic character of a protein, J. Mol. Biol. 157 (1982) 105-132.
99. B. Lee, F.M. Richards, The interpretation of protein structures: estimation of static accessibility, J. Mol. Biol. 55 (1971) 379-400.
100. P. Narang, K. Bhushan, S. Bose, B. Jayaram, Protein structure evaluation using allatom energy based empirical scoring function, J. Biomol. Struct. Dyn. 23 (2006) 385-406. (Pubitemid 43099652)
101. N. Jayaram B. Arora, Energetics of base pairs in B-DNA in solution: an appraisal of potential functions and dielectric treatments, J. Phys. Chem. 102 (1998) 6139-6144.
102. N. Arora, B. Jayaram, Strength of hydrogen bonds in alpha helices, J. Comput. Chem. 18 (1997) 1245-1252. (Pubitemid 127650579)
103. M.A. Young, B. Jayaram, D.L. Beveridge, Local dielectric environment of B-DNA in solution: results from a 14 nanosecond molecular dynamics trajectory, J. Phys. Chem. 102 (1998) 7666-7669. (Pubitemid 128578404)
104. D. Rykunov, A. Fiser, New statistical potential for quality assessment of protein models and a survey of energy functions, BMC Bioinform. 11 (2010) 28.
105. Q. Fang, D. Shortle, Protein refolding in silico with atom-based statistical potentials and conformational search using a simple genetic algorithm, J. Mol. Biol. 359 (5) (2006) 1456.
106. B.J. McConkey, V. Sobolev, M. Edelman, Discrimination of native protein structures using atom-atom contact scoring, Proc. Natl. Acad. Sci. U. S. A. 100 (6) (2003) 215.
107. P. Benkert, M. Kunzli, T. Schwede, QMEAN server for protein model quality estimation, Nucleic Acids Res. (2009), http://dx.doi.org/10.1093/nar/gkp322.
108. P. Benkert, S.C. Tosatto, D. Schomburg, QMEAN: a comprehensive scoring function for model quality assessment, Proteins 71 (1) (2008) 261-277. (Pubitemid 351358609)
109. B.J. McConkey, V. Sobolev, M. Edelman, Discrimination of native protein structures using atom-atom contact scoring, Proc. Natl. Acad. Sci. U. S. A. 100 (6) (2003) 3215.
110. J. Zhang, R. Chen, J. Liang, Empirical potential function for simplified protein models: combining contact and local sequence-structure descriptors, Proteins: Struct. Funct. Bioinform. 63 (4) (2006) 949-960. (Pubitemid 43765146)
111. M. Lu, A.D. Dousis, J. Ma, OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing, J. Mol. Biol. 376 (1) (2008) 288-301.
112. D. Rykunov, A. Fiser, Effects of amino acid composition, finite size of proteins, and sparse statistics on distance-dependent statistical pair potentials, Proteins: Struct. Funct. Bioinform. 67 (3) (2007) 59-568.
113. J.C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R.D. Skeel, L. Kale, K. Schulten, Scalable molecular dynamics with NAMD, J. Comput. Chem. 26 (16) (2005) 781-1802.
114. Q. Fang, D. Shortle, A consistent set of statistical potentials for quantifying local side-chain and backbone interactions, Proteins 60 (1) (2005) 90.
115. M.Y. Shen, A. Sali, Statistical potential for assessment and prediction of protein structures, Protein Sci. 15 (11) (2006) 2507-2524. (Pubitemid 44771688)
116. M.J. Sippl, Recognition of errors in three-dimensional structures of proteins, Proteins 17 (4) (1993) 355.
117. Liqing Tian, Wu. Aiping, Yang Cao, Xiaoxi Dong, Hu. Yun, Taijiao Jiang, NCACO-score: an effective main-chain dependent scoring function for structure modeling, BMC Bioinform. 1 (2) (2011) 208.
118. Y. Makino, N. Itoh, A knowledge-based structure-discriminating function that requires only main-chain atom coordinates, BMC Struct. Biol. 8 (2008) 46.
119. H. Zhou, Y. Zhou, Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction, Protein Sci. 11 (11) (2002) 2714-2726. (Pubitemid 35191145)
120. H. Lu, J. Skolnick, A distance-dependent atomic knowledge-based potential for improved protein structure selection, Proteins 44 (2001) 223-232. (Pubitemid 32702231)
121. R. Samudrala, J. Moult, An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction, J. Mol. Biol. 275 (5) (1998) 895-916. (Pubitemid 28077703)
122. A. Godzik, A. Kolinski, J. Skolnick, Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets, Protein Sci. 4 (10) (1995) 2107-2117.
123. U. Bastolla, J. Farwer, E.W. Knapp, M. Vendruscolo, How to guarantee optimal stability for most representative structures in the Protein Data Bank, Proteins 44 (2) (2001) 79-96.
124. J. Skolnick, L. Jaroszewski, A. Kolinski, A. Godzik, Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct? Protein Sci. 6 (3) (1997) 676-688. (Pubitemid 27120064)
125. B. Park, M. Levitt, Energy functions that discriminate X-ray and near native folds from well-constructed decoys, J. Mol. Biol. 258 (2) (1996) 367-392. (Pubitemid 26131738)
126. J. Skolnick, A. Kolinski, A. Ortiz, Derivation of protein-specific pair potentials based on weak sequence fragment similarity, Proteins 38 (1) (2000) 3-16. (Pubitemid 30020598)
127. M.R. Betancourt, D. Thirumalai, Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes, Protein Sci. 8 (2) (1999) 361-369. (Pubitemid 29072436)
128. P.D. Thomas, K.A. Dill, An iterative method for extracting energy-like quantities from protein structures, Proc. Natl. Acad. Sci. U. S. A. 93 (21) (1996) 11628-11633. (Pubitemid 26347173)
129. S. Miyazawa, R.L. Jernigan, Estimation of effective inter residue contact energies from protein crystal structures: quasi-chemical approximation, Macromolecules 18 (3) (1985) 534-552.
130. S. Miyazawa, R.L. Jernigan, Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading, J. Mol. Biol. 256 (3) (1996) 623-644. (Pubitemid 26107211)
131. S. Miyazawa, R.L. Jernigan, Self-consistent estimation of inter-residue protein contact energies based on an equilibrium mixture approximation of residues, Proteins 34 (1) (1999) 49-68. (Pubitemid 29019531)
132. L.A. Mirny, E.I. Shakhnovich, How to derive a protein folding potential? A new approach to an old problem, J. Mol. Biol. 264 (5) (1996) 1164-1179. (Pubitemid 27019500)
133. K.T. Simons, I. Ruczinski, C. Kooperberg, B.A. Fox, C. Bystroff, D. Baker, Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins, Proteins 34 (1) (1999) 82-95. (Pubitemid 29019533)
134. K.T. Simons, C. Kooperberg, E. Huang, D. Baker, Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions, J. Mol. Biol. 268 (1) (1997) 209-225. (Pubitemid 27192690)
135. D. Tobi, G. Shafran, N. Linial, R. Elber, On the design and analysis of protein folding potentials, Proteins 40 (1) (2000) 71-85. (Pubitemid 30368583)
136. Y. Feng, A. Kloczkowski, R.L. Jernigan, Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys, Proteins 68 (1) (2007) 57-66. (Pubitemid 46876534)
137. S. Tanaka, H.A. Scheraga, Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins, Macromolecules 9 (6) (1976) 945-950.
138. M. Vendruscolo, E. Domany, Pairwise contact potentials are unsuitable for protein folding, J. Chem. Phys. 109 (24) (1998) 11101-11108. (Pubitemid 128675160)
139. I. Bahar, M. Kaplan, R.L. Jernigan, Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches, Proteins 29 (3) (1997) 292-308. (Pubitemid 27484221)
140. B. Robson, D.J. Osguthorpe, Refined models for computer simulation of protein folding. Applications to the study of conserved secondary structure and flexible hinge points during the folding of pancreatic trypsin inhibitor, J. Mol. Biol. 132 (1) (1979) 19-51.