ICOSA: A Distance-Dependent, Orientation-Specific Coarse-Grained Contact Potential for Protein Structure Modeling

Journal of Molecular Biology

Volumn 427, Issue 15, 2015, Pages 2562-2576

  Elhefnawy, Wessam ^a   Chen, Lin ^a   Han, Yun ^a   Li, Yaohang ^a  

^a Old Dominion University   (United States)

Author keywords

contact orientation and distance; finite ideal gas reference state; icosahedrons; inter residue contact; knowledge based potential

Indexed keywords

ARTICLE; MEASUREMENT ACCURACY; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STRUCTURE; SENSITIVITY ANALYSIS; STRUCTURE ANALYSIS; ALGORITHM; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; KNOWLEDGE BASE; PROCEDURES; PROTEIN PROTEIN INTERACTION; SEQUENCE ANALYSIS;

CASPASE 10;

ALGORITHMS; CASPASE 10; COMPUTATIONAL BIOLOGY; KNOWLEDGE BASES; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPPING; PROTEIN INTERACTION MAPS; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 84937812327     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2015.05.022     Document Type: Article

References (70)

1. M. Vendruscolo, and E. Domany Pairwise contact potentials are unsuitable for protein folding J Chem Phys 109 1998 11101 11108
2. M. Vendruscolo, R. Najmanovich, and E. Domany Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading? Proteins 38 2000 134 148
3. L.A. Mirny, and E.I. Shakhnovich How to derive a protein folding potential? A new approach to an old problem J Mol Biol 264 1996 1164 1179
4. J. Khatun, S.D. Khare, and N.V. Dokholyan Can contact potentials reliably predict stability of proteins? J Mol Biol 336 2004 1223 1238
5. B. Park, and M. Levitt Energy functions that discriminate X-ray and near-native folds from well-constructed decoys J Mol Biol 258 1996 367 392
6. S.T. Wu, A. Szilagyi, and Y. Zhang Improving protein structure prediction using multiple sequence-based contact predictions Structure 19 2011 1182 1191
7. W.P. Russ, and R. Ranganathan Knowledge-based potential functions in protein design Curr Opin Struc Biol 12 2002 447 452
8. D.V.S. Ravikant, and R. Elber Energy design for protein-protein interactions J Chem Phys 135 2011 10.1063/1.3615722
9. S. Miyazawa, and 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 1996 623 644
10. M.R. Betancourt, and 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 1999 361 369
11. J. Skolnick, A. Kolinski, and A. Ortiz Derivation of protein-specific pair potentials based on weak sequence fragment similarity Proteins 38 2000 3 16
12. H.Y. Zhou, and Y.Q. Zhou Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction Protein Sci 11 2002 2714 2726
13. H. Lu, and J. Skolnick A distance-dependent atomic knowledge-based potential for improved protein structure selection Proteins 44 2001 223 232
14. M. Berrera, H. Molinari, and F. Fogolari Amino acid empirical contact energy definitions for fold recognition in the space of contact maps BMC Bioinformatics 4 2003 8
15. C. Zhang, G. Vasmatzis, J.L. Cornette, and C. DeLisi Determination of atomic desolvation energies from the structures of crystallized proteins J Mol Biol 267 1997 707 726
16. R. Zimmer, M. Wohler, and R. Thiele New scoring schemes for protein fold recognition based on Voronoi contacts Bioinformatics 14 1998 295 308
17. B.J. McConkey, V. Sobolev, and M. Edelman Discrimination of native protein structures using atom-atom contact scoring Proc Natl Acad Sci USA 100 2003 3215 3220
18. J. Esque, S. Leonard, A.G. de Brevern, and C. Oguey VLDP Web server: a powerful geometric tool for analysing protein structures in their environment Nucleic Acids Res 41 2013 W373 W378
19. R.K. Singh, A. Tropsha, and I.I. Vaisman Delaunay tessellation of proteins: four body nearest-neighbor propensities of amino acid residues J Comput Biol 3 1996 213 221
20. G.M. Reck, and I.I. Vaisman Decoy discrimination using contact potentials based on Delaunay tessellation of hydrated proteins The 4th International Symposium on Voronoi Diagrams in Science and Engineering 2007 158 167
21. X. Li, C.Y. Hu, and J. Liang Simplicial edge representation of protein structures and alpha contact potential with confidence measure Proteins 53 2003 792 805
22. X. Li, and J. Liang Geometric cooperativity and anticooperativity of three-body interactions in native proteins Proteins Struct Funct Bioinf 60 2005 46 65
23. J. Esque, C. Oguey, and A.G. de Brevern Comparative analysis of threshold and tessellation methods for determining protein contacts J Chem Inf Model 51 2011 493 507
24. L. Brocchieri, and S. Karlin How are close residues of protein structures distributed in primary sequence? Proc Natl Acad Sci USA 92 1995 12136 12140
25. G. Faure, A. Bornot, and A.G. de Brevern Protein contacts, inter-residue interactions and side-chain modelling Biochimie 90 2008 626 639
26. C. Zhang, and S.H. Kim Environment-dependent residue contact energies for proteins Proc Natl Acad Sci USA 97 2000 2550 2555
27. A. Rojnuckarin, and S. Subramaniam Knowledge-based interaction potentials for proteins Proteins 36 1999 54 67
28. F. Zhao, and J. Xu A position-specific distance-dependent statistical potential for protein structure and functional study Structure 20 2012 1118 1126
29. M.J. Duan, and Y.H. Zhou A contact energy function considering residue hydrophobic environment and its application in protein fold recognition Genomics Proteomics Bioinformatics 3 2005 218 224
30. Y.P. Feng, A. Kloczkowski, and R.L. Jernigan Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys Proteins Struct Funct Bioinf 68 2007 57 66
31. P.J. Munson, and R.K. Singh Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment Protein Sci 6 1997 1467 1481
32. I. Bahar, and R.L. Jernigan Coordination geometry of nonbonded residues in globular proteins Fold Des 1 1996 357 370
33. N.V. Buchete, J.E. Straub, and D. Thirumalai Anisotropic coarse-grained statistical potentials improve the ability to identify nativelike protein structures J Chem Phys 118 2003 7658 7671
34. A. Mukherjee, P. Bhimalapuram, and B. Bagchi Orientation-dependent potential of mean force for protein folding J Chem Phys 123 2005 014901
35. Y. Makino, and N. Itoh A knowledge-based structure-discriminating function that requires only main-chain atom coordinates BMC Struct Biol 8 2008 10.1186/1472-6807-8-46
36. D. Rykunov, and A. Fiser New statistical potential for quality assessment of protein models and a survey of energy functions BMC Bioinformatics 11 2010 128
37. S.E. Moughon, and R. Samudrala LoCo: a novel main chain scoring function for protein structure prediction based on local coordinates BMC Bioinformatics 12 2011 368
38. M.J. Sippl Calculation of conformational ensembles from potentials of mean force - an approach to the knowledge-based prediction of local structures in globular proteins J Mol Biol 213 1990 859 883
39. S. Miyazawa, and R.L. Jernigan Estimation of effective interresidue contact energies from protein crystal structures - quasi-chemical approximation Macromolecules 18 1985 534 552
40. R. Samudrala, and J. Moult An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction J Mol Biol 275 1998 895 916
41. J. Skolnick, L. Jaroszewski, A. Kolinski, and A. Godzik Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct? Protein Sci 6 1997 676 688
42. J. Zhang, and Y. Zhang A novel side-chain orientation dependent potential derived from random-walk reference state for protein fold selection and structure prediction PLoS One 5 2010 e15386
43. H.Y. Deng, Y. Jia, Y.Y. Wei, and Y. Zhang What is the best reference state for designing statistical atomic potentials in protein structure prediction? Proteins Struct Funct Bioinf 80 2012 2311 2322
44. M.Y. Shen, and A. Sali Statistical potential for assessment and prediction of protein structures Protein Sci 15 2006 2507 2524
45. J. Tsai, R. Bonneau, A.V. Morozov, B. Kuhlman, C.A. Rohl, and D. Baker An improved protein decoy set for testing energy functions for protein structure prediction Proteins 53 2003 76 87
46. A. Kryshtafovych, B. Monastyrskyy, and K. Fidelis CASP prediction center infrastructure and evaluation measures in CASP10 and CASP ROLL Proteins Struct Funct Bioinf 82 2014 7 13
47. M.Y. Lu, A.D. Dousis, and J.P. Ma OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing J Mol Biol 376 2008 288 301
48. K.T. Simons, C. Kooperberg, E. Huang, and D. Baker Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions J Mol Biol 268 1997 209 225
49. A. Zemla LGA: a method for finding 3D similarities in protein structures Nucleic Acids Res 31 2003 3370 3374
50. Y.P. Feng, A. Kloczkowski, and R.L. Jernigan Potentials 'R'Us Web-server for protein energy estimations with coarse-grained knowledge-based potentials BMC Bioinformatics 11 2010 92
51. M. Boniecki, P. Rotkiewicz, J. Skolnick, and A. Kolinski Protein fragment reconstruction using various modeling techniques J Comput Aid Mol Des 17 2003 725 738
52. D. Tobi, G. Shafran, N. Linial, and R. Elber On the design and analysis of protein folding potentials Proteins 40 2000 71 85
53. S. Miyazawa, and R.L. Jernigan Self-consistent estimation of inter-residue protein contact energies based on an equilibrium mixture approximation of residues Proteins 34 1999 49 68
54. S. Tanaka, and H.A. Scheraga Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins Macromolecules 9 1976 945 950
55. U. Bastolla, J. Farwer, E.W. Knapp, and M. Vendruscolo How to guarantee optimal stability for most representative structures in the protein data bank Proteins 44 2001 79 96
56. P.D. Thomas, and K.A. Dill An iterative method for extracting energy-like quantities from protein structures Proc Natl Acad Sci USA 93 1996 11628 11633
57. B. Robson, and 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 1979 19 51
58. A. Godzik, A. Kolinski, and J. Skolnick Are proteins ideal mixtures of amino acids - analysis of energy parameter sets Protein Sci 4 1995 2107 2117
59. S.H. Bryant, and C.E. Lawrence An empirical energy function for threading protein sequence through the folding motif Proteins 16 1993 92 112
60. K.T. Simons, I. Ruczinski, C. Kooperberg, B.A. Fox, C. Bystroff, and D. Baker Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins Proteins 34 1999 82 95
61. I. Bahar, M. Kaplan, and R.L. Jernigan Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches Proteins 29 1997 292 308
62. W.L. Jorgensen, D.S. Maxwell, and J. TiradoRives Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids J Am Chem Soc 118 1996 11225 11236
63. A. Ghosh, C.S. Rapp, and R.A. Friesner Generalized born model based on a surface integral formulation J Phys Chem B 102 1998 10983 10990
64. I.A. Rata, Y.H. Li, and E. Jakobsson Backbone statistical potential from local sequence-structure interactions in protein loops J Phys Chem B 114 2010 1859 1869
65. Y.H. Li, H. Liu, I. Rata, and E. Jakobsson Building a knowledge-based statistical potential by capturing high-order inter-residue interactions and its applications in protein secondary structure assessment J Chem Inf Model 53 2013 500 508
66. C. Yanover, N. Vanetik, M. Levitt, R. Kolodny, and C. Keasar Redundancy-weighting for better inference of protein structural features Bioinformatics 30 2014 2295 2301
67. G.L. Wang, and R.L. Dunbrack PISCES: a protein sequence culling server Bioinformatics 19 2003 1589 1591
68. Y. Feng, R.L. Jernigan, and A. Kloczkowski Orientational distributions of contact clusters in proteins closely resemble those of an icosahedron Proteins Struct Funct Bioinf 73 2008 730 741
69. M.J. Sippl Knowledge-based potentials for proteins Curr Opin Struc Biol 5 1995 229 235
70. P.D. Thomas, and K.A. Dill Statistical potentials extracted from protein structures: how accurate are they? J Mol Biol 257 1996 457 469