PIE-efficient filters and coarse grained potentials for unbound protein-protein docking

Proteins: Structure, Function and Bioinformatics

Volumn 78, Issue 2, 2010, Pages 400-419

  Ravikant, D V S ^a   Elber, Ron ^a,b  

^a Department of Computer Science and School of Operations Research and Information Engineering   (United States)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

Linear programming; Protein docking; Ranking decoys; Scoring function

Indexed keywords

ARTICLE; COMPLEX FORMATION; MATHEMATICAL MODEL; MOLECULAR DOCKING; MOLECULAR MODEL; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; ALGORITHM; BIOLOGICAL MODEL; CHEMISTRY; COMPUTER PROGRAM; COMPUTER SIMULATION; METABOLISM; PROTEIN BINDING; PROTEIN CONFORMATION;

PROTEIN;

ALGORITHMS; COMPUTER SIMULATION; MODELS, BIOLOGICAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEINS; SOFTWARE;

EID: 77449134208     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22550     Document Type: Article

References (53)

1. Söllner T, Bennett MK, Whiteheart SW, Scheuer RH, Rothman JE. A protein assembly-disassembly pathway in vitro that may correspond to sequential steps of synaptic vesicle docking, activation, and fusion. Cell 1993;75:409-418.
2. Arents G, Burlingame RW, Wang BC, Love WE, Moudrianakis EN. The nucleosomal core histone octamer at 3.1 A resolution: a tripartite protein assembly and a left-handed superhelix, Proc Natl Acad Sci U S A 1991;88:10148-10152.
3. Lesné S, Koh MT, Kotilinek L, Kayed R, Glabe CG, Yang A, Gallagher M, Ashe KH. A specific amyloid-β protein assembly in the brain impairs memory. Nature 2006;440:352-357.
4. Sachs K, Perez O, Pe'er D, Lauffenburger DA, Nolan GP. Causal, protein-signaling networks derived from multiparameter single-cell data. Science 2005;308:523-529.
5. Hamm HE. The many faces of G protein signaling. J Biol Chem 1998;273:669-672.
6. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston. M, Fields S, Romberg JM. A. comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000;403:623-627.
7. Gandhi TKB, Zhong J, Mathivanan S, Karthick L, Chandrika KN, Mohan SS, Sharma S, Pinkert S, Nagaraju S, Periaswamy B, Mishra G, Nandakumar K, Shen. B, Deshpande N, Nayak R, Sarker M, Boeke JD, Parmigiani G, Schultz J, Bader JS, Pandey A. Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet 2006;38:285-293.
8. Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, Li Y, Hao YL, Ooi CE, Godwin B, Vitols E, Vijayadamodar G, Pochart P, Machineni H, Welsh M, Kong Y, Zerhusen B, Malcolm R, Varrone Z, CoIKs A, Minto M, Burgess S, McDaniel L, Stimpson. E, Spriggs F, Williams J, Neurath. K, Ioime N, Agee M, Voss E, Furtak K, Renzulli R, Aanensen N, Carrolla S, Bickelhaupt E, Lazovatsky Y, DaSilva A, Zhong J, Stanyon. CA, Finley RL, Jr.; White KP, Braverman M, Jarvie T, Gold S, Leach M, Knight J, Shimkets RA, McKenna MP, Chant J, Rothberg JM. A protein interaction map of Drosophila melanogaster. Science 2003;302:1727-1736.
9. Wodak SJ, Janin J. Computer analysis of protein-protein interaction. J Mol Biol 1978;124:323-342.
10. Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem AA, Aflalo C, Vakser IA. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci U S A 1992;89:2195-2199.
11. Fischer D, Lin SL, Wolfson HJ, Nussinov R. A Geometry-based suite of molecular docking processes. J Mol Biol 1995;248:459-477.
12. Abagyan R, Totrov M, Kuznetsov D. ICM-a new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation. J Comput Chem 1994;15:488-506.
13. Gabb HA, Jackson RM, Sternberg MJE. Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol 1997;272:106-120.
14. Ritchie DW, Kemp GJL. Protein docking using spherical polar Fourier correlations. Proteins 2000;39:178-194.
15. Chen R, Weng Z. Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins 2002;47:281-294.
16. Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 2003;331:281-299.
17. Palma PN, Krippahi L, Wampler JE, Moura JJG. BiGGER: a new (soft) docking algorithm for predicting protein interactions. Proteins 2000;39:372-384.
18. Mandeli JG, Roberts VA, Pique ME, Kotlovyi V, Mitchell JC, Nelson E, TMgelny I, Ten Eyck LF. Protein docking using continuum electrostatics and geometric fit. Protein Eng 200.1; 14:105-113.
19. Camacho CJ, Vajda S. Protein docking along smooth association pathways. Proc Natl Acad Sci U S A 2001;98:10636-10641.
20. Moont G, Gabb HA, Sternberg MJE. Use of pair potentials across protein interfaces in screening predicted docked complexes. Proteins 1999;35:364-373.
21. Keskin O, Bahar I, Badretdinov AY, Ptitsyn. OB, Jernigan. RL. Empirical solvent-mediated potentials hold for both intra-molecular and inter-molecular inter-residue interactions. Protein Sci 1998:7:25782586.
22. Glaser F, Steinberg DM, Vakser IA, Ben-Tal N. Residue frequencies and pairing preferences at protein-protein interfaces. Proteins 2001; 43:89-102.
23. Lu H, Lu L, Skolnick J. Development of unified statistical potentials describing protein-protein interactions. Biophys J 2003;84:1895-1901.
24. Miyazawa S, Jernigan RL. .Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 1985;18:534-552.
25. Maiorov VN, Grippen GM. Contact potential that recognizes the correct folding of globular proteins. J Mol Biol 1992;227:876-888.
26. Vendruscolo M, Najmanovich R, Domany E. Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading? Proteins 2000;38:134-148.
27. Tobi D, Shafran. G, Linial N, Elber R. On the design and analysis of protein folding potentials. Proteins 2000;40:71-85.
28. Tobi. D, Bahar I. Optimal design of protein docking potentials: efficiency and limitations. Proteins 2006;62:970-981.
29. Bordner AJ, Gorin AA. Comprehensive inventory of protein complexes in the Protein Data Bank from, consistent classification, of interfaces. BMC Bioinformatics 2008;9:234.
30. Robert CH, Janin J. A soft, mean-field potential derived from crystal contacts for predicting protein-protein interactions. J Mol Biol 1998;283:1037-1047.
31. Liu S, Zhang C, Zhou H, Zhou Y. A. physical reference state unifies the structure-derived potential of mean, force for protein folding and binding. Proteins 2004;56:93-101.
32. Martin O, Schomburg D. Efficient comprehensive scoring of docked protein complexes using probabilistic support vector machines. Proteins 2008;70:1367-1378.
33. Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z. Protein-protein docking benchmark 20: an update. Proteins 2005:60:214-216.
34. LeGrand SM, Merz KM. Rapid approximation to molecular surface area via the use of Boolean logic and look-up tables. J Comput Chem 1993;14:349-352.
35. Jorgensen WL, Tirado-Rives J. The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. J Am Chem Soc 1988;110:1657-1666.
36. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 1997;25:3389-3402.
37. Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 1970;48:443-453.
38. Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A. Comparative protein structure modeling using MODELLER. In: Coligan JE, Dunn BM, Speicher DW, Wingfield PT, editors. Current protocols in protein science. Hoboken, NJ: John Wiley & Sons, Inc; 2007:291-2931.
39. Wagner M, Meiler J, Elber R. Large-scale linear programming techniques for the design of protein folding potentials. Math Prog 2004; 101:301-318.
40. Zhang Y, Skoinick J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 2005;33:2302-2309.
41. Mintseris J, Pierce B, Wiehe K, Anderson R, Chen R, Weng Z. Integrating statistical pair potentials into protein complex prediction. Proteins 2007;69:511-520.
42. Duhovny D, Nussinov R, Woifson HJ. Efficient unbound docking of rigid molecules. Proceedings of the Second International Workshop on Algorithms in Bioinformatics. New York. Springer-Verlag; 2002.
43. Pierce B, Weng Z. ZRANK: reranking protein docking predictions with an optimized energy function. Proteins 2007;67:1078-1086.
44. Méndez R, Leplae R, Maria LD, Wodak SJ. Assessment of blind predictions of protein-protein, interactions: current status of docking methods. Proteins 2003;52:51-67.
45. Pierce B, Weng Z. A combination of rescoring and refinement significantly improves protein docking performance. Proteins 2008;72:270279.
46. Boeckmann B, Bairoch A, Apweiler R, Blatter M-C, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 2003;31:365-370.
47. Chuang G-Y, Kozakov D, Brenke R, Comeau SR, Vajda. S. DARS (decoys as the reference state) potentials for protein-protein docking. Biophys J 2008;95:4217-4227.
48. Kabsch W, Sander C. Dictionary of protein secondary structure; pattern recognition of hydrogen-bonded and geometrical, features. Biopolymers 1983;22:2577-2637.
49. Pinak Chakrabarti JJ. Dissecting protein-protein recognition sites. Proteins 2002;47:334-343.
50. Ranjit PB, Dissecting subunit interfaces in homodimeric proteins. Proteins 2003;53:708-719.
51. Anashklna A, Kuznetsov E, Esipova N, Tumanyan V. Comprehensive statistical analysis of residues interaction specificity at proteinprotein interfaces. Proteins 2007;67:1060-1077.
52. Mintseris J, Weng Z. Atomic contact vectors in protein-protein recognition. Proteins 2003;53:629-639.
53. Ansari S, Helms V. Statistical analysis of predominantly transient protein-protein interfaces. Proteins 2005;61:344-355.