Docking protein domains in contact space

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Lise, Stefano ^a   Walker Taylor, Alice ^a   Jones, David T ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EVOLUTIONARY INFORMATION; EXPERIMENTAL INVESTIGATIONS; FULL THREE-DIMENSIONAL; FUNCTIONAL ASSOCIATIONS; PHYSICAL INTERACTIONS; PROTEIN CONFORMATIONAL CHANGES; PROTEIN-PROTEIN INTERACTIONS; SIMULATED ANNEALING ALGORITHMS;

COMPUTATIONAL METHODS; MOLECULAR STRUCTURE;

PROTEINS;

DOCKING PROTEIN; PROTEIN; PROTEIN BINDING;

ALGORITHM; ARTICLE; BINDING SITE; CONFORMATIONAL TRANSITION; FUNCTIONAL PROTEOMICS; MATHEMATICAL COMPUTING; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SCORING SYSTEM; STATISTICAL ANALYSIS; AMINO ACID SEQUENCE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; MOLECULAR GENETICS; PROCEDURES; PROTEIN TERTIARY STRUCTURE; SEQUENCE ANALYSIS;

RUMEX;

ALGORITHMS; AMINO ACID SEQUENCE; BINDING SITES; COMPUTER SIMULATION; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SEQUENCE ANALYSIS, PROTEIN;

EID: 33748300623     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-310     Document Type: Article

References (63)

1. Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P: Molecular biology of the cell fourth edition. New York: Garland Science; 2002.
2. Kleanthous C, Ed: Protein-protein Recognition Edited by: Hames BD, Glover DM. Oxford: Oxford University Press; 2000. Frontiers in Molecular Biology
3. Wodak SJ, Janin J: Structural basis of macromolecular recognition. Advances in Protein Chemistry 2002, 61:9-73.
4. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Research 2000, 28:235-242.
5. Aloy P, Pichaud M, Russell RB: Protein complexes: structure prediction challenges for the 21st century. Current Opinion in Structural Biology 2005, 15:15-22.
6. Szilagyi A, Grimm V, Arakaki A, Skolnick J: Prediction of physical protein-protein interactions. Physical Biology 2005, 2:S1-S16.
7. Smith GR, Sternberg MJE: Prediction of protein-protein interactions by docking methods. Current Opinion in Structural Biology 2002, 12:28-35.
8. Arkin MR, Wells JA: Small-molecule inhibitors of protein-protein interactions: progressing towards the dream. Nature Reviews Drug Discovery 2004, 3:301-317.
9. Jones S, Marin A, Thornton JM: Protein domain interfaces: characterization and comparison with oligomeric protein interfaces. Protein Engineering 2000, 13:77-82.
10. Park J, Lappe M, Teichmann SA: Mapping Protein Family Interactions: Intramolecular and Intermolecular Protein Family Interaction Repertoires in the PDB and Yeast. Journal of Molecular Biology 2001, 307:929-938.
11. Littler SJL, Hubbard SJ: Conservation of Orientation and Sequence in Protein Domain-Domain Interactions. Journal of Molecular Biology 2005, 345:1265-1279.
12. Shoemaker BA, Panchenko AR, Bryant SH: Finding biologically relevant protein domain interactions: Conserved binding mode analysis. Protein Science 2006, 15:352-361.
13. Schueler-Furman O, Wang C, Bradley P, Misura K, Baker D: Progress in Modeling of Protein Structures and Interactions. Science 2005, 310:638-642.
14. Halperin I, Ma B, Wolfson H, Nussinov R: Principles of Docking: An Overview of Search Algorithms and a Guide to Scoring Functions. Proteins 2002, 47:409-443.
15. Janin J, Henrick K, Moult J, Eyck LT, Sternberg MJE, Vajda S, Vakser I, Wodak SJ: CAPRI: A Critical Assessment of PRedicted Interactions. Proteins 2003, 52:2-9.
16. Méndez R, Leplae R, Lensink MF, Wodak SJ: Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins 2005, 60:150-169.
17. Wodak SJ, Méndez R: Prediction of protein-protein interactions: the CAPRI experiment, its evaluation and implications. Current Opinion in Structural Biology 2004, 14:242-249.
18. van Dijk ADJ, Boelens R, Bonvin AMJJ: Data-driven docking for the study of biomolecular complexes. FEBS Journal 2005, 272:293-312.
19. Reš I, Lichtarge O: Chracter and evolution of protein-protein interfaces. Physical Biology 2005, 2:S36-S43.
20. Fariselli P, Pazos F, Valencia A, Casadio R: Prediction of protein-protein interaction sites in heterocomplexes with neural networks. Eur J Biochem 2002, 269:1356-1361.
21. Koike A, Takagi T: Prediction of protein-protein interaction sites using support vector machines. Protein Eng Des Sel 2004, 17:165-173.
22. Sen TZ, Kloczkowski A, Jernigan RL, Yan C, Honavar V, Ho KM, Wang CZ, Ihm Y, Cao H, Gu X, Dobbs D: Predicting binding sites ofhydrolase-inhibitor complexes by combining several methods. BMC Bioinformatics 2004, 5:205.
23. Bradford JR, Westhead DR: Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics 2005, 21:1487-1494.
24. Clackson T, Wells JA: A Hot Spot of Binding Energy in a Hormone-Receptor Interface. Science 1995, 267:383-386.
25. DeLano WL: Unraveling hot spots in binding interfaces: progress and challenges. Current Opinion in Structural Biology 2002, 12:14-20.
26. Hu Z, Ma B, Wolfson H, Nussinov R: Conservation of Polar Residues as Hot Spots at Protein Interfaces. Proteins 2000, 39:331-342.
27. Ma B, Elkayam T, Wolfson H, Nussinov R: Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc Natl Acad Sci U S A 2003, 100:5772-5777.
28. Bogan AA, S TK: Anatomy of Hot Spots in Protein Interfaces. Journal of Molecular Biology 1998, 280:1-9.
29. Li X, Keskin O, Ma B, Nussinov R, Liang J: Protein-Protein Interactions: Hot Spots and Structurally Conserved Residues often Locate in Complemented Pockets that Pre-organized in the Unbound States: Implications for Docking. Journal of Molecular Biology 2004, 344:781.
30. Fernandéz A, Scheraga HA: Insufficiently dehydrated hydrogen bonds as determinants of protein interactions. Proc Natl Acad Sci U S A 2003, 100:113-118.
31. Rajamani D, Thiel S, Vajda S, Camacho CJ: Anchor residues in protein-protein interactions. Proc Natl Acad of Sci USA 2004, 101:11287-11292.
32. Halperin I, Wolfson H, Nussinov R: Protein-Protein'Interactions: Coupling of Structurally Conserved Residues and of Hot Spots across Interfaces. Implications for Docking. Structure 2004, 12:1027-1038.
33. Duan Y, Reddy BVB, Kaznessis YN: Physicochemical and residue conservation calculations to improve the ranking of protein-protein docking solutions. Protein Science 2005, 14:316-328.
34. Caffrey DR, Somaroo S, Hughes JD, Mintseris J, S HE: Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? Protein Science 2004, 13:190-202.
35. Tovchigrechko A, Vakser IA: Development and Testing of an Automated Approach to Protein Docking. Proteins 2005, 60:296-301.
36. Aloy P, Querol E, Aviles FX, Sternberg MJE: Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. Journal of Molecular Biology 2001, 311:395-408.
37. Tress M, de Juan D, Graña O, Gómez MJ, Gómez-Puertas P, González JM, López G, Valencia A: Scoring Docking Models With Evolutionary Information. Proteins 2005, 60:275-280.
38. Chelliah V, Blundell TL, Fernández-Recio J: Efficient Restraints for Protein-Protein Docking by Comparison of Observed Amino Acid Substitution Patterns with those Predicted from Local Environment. Journal of Molecular Biology 2006, 357:1669-1682.
39. de Vries SJ, van Dijk ADJ, Bonvin AMJJ: WHISCY: What information does surface conservation yield? Application to data-driven docking. Proteins 2006, 63:479-489.
40. Holm L, Sander C: Protein Structure Comparison by Alignment of Distance Matrices. Journal of Molecular Biology 1993, 233:123-138.
41. Godzik A, Skolnick J, Kolinski A. Regularities in interaction patterns of globular proteins. Protein Engineering 1993, 6:801-810.
42. Vendruscolo M, Domany E: Protein folding using contact maps. Vitam Horm 2000, 58:171-212.
43. Tovchigrechko A, Wells CA, Vakser IA: Docking of protein models. Protein Science 2002, 11:1888-1896.
44. Wodak SJ, De Crombrugghe M, Janin J: Computer studies of interactions between macromolecules. Progress in Biophysics and Molecular Biology 1987, 49:29-63.
45. Cherfils J, Janin J: Protein docking algorithms: simulating molecular recognition. Current Opinion in Structural Biology 1993, 3:265-269.
46. Echols N, Milburn D, Gerstein M: MolMovDB: analysis and visualization of conformational change and structural flexibility. Nucleic Acids Res 2003, 31:478-82.
47. Pearl F, Todd A, Sillitoe I, Dibley M, Redfern O, Lewis T, Bennett C, Marsden R, Grant A, Lee D, Akpor A, Maibaum M, Harrison A, Dallman T, Reeves G, Diboun I, Addou S, Lise S, Johnston C, Sillero A, Thornton J, Orengo C: The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. Nucleic Acids Research 2005, 33:D247-D251.
48. Martin ACR: ProFit. [http://www.bioinf.org.uk/software/profit/].
49. Kelley LA, Gardner SP, Sutcliffe MJ: An Automated Approach For Clustering An Ensemble Of NMR-Derived Protein Structures Into Conformationally-Related Subfamilies. Protein Engineering 1996, 9:1063-1065.
50. Fiser A, Sali A: ModLoop: automated modeling of loops in protein structures. Bioinformatics 2003, 19:2500-2501.
51. Méndez R, Leplae R, De Maria L, Wodak SJ: Assessment of Blind Predictions of Protein-Protein Interactions: Current Status of Docking Methods. Proteins 2003, 52:51-67.
52. Janin J: Assessing predictions of protein-protein interaction: The CAPRI experiment. Protein Science 2005, 14:278-283.
53. Sanner MF, Olson AJ, Spehner JC: Reduced Surface: An Efficient Way to Compute Molecular Surfaces. Biopolymers 1996, 38:305-320.
54. Connolly ML: Measurement of protein surface shape by solid angles. J Mol Graphics 1986, 4:3-6.
55. Norel R, Lin SL, Wolfson HJ, Nussinov R: Shape Complementarity at Protein-Protein Interfaces. Biopolymers 1994, 34:933-940.
56. Norel R, Petrey D, Wolfson HJ, Nussinov R: Examination of shape complementarity in docking of Unbound proteins. Proteins 1999, 36:307-317.
57. Moont G, Gabb HA, Sternberg MJE: Use of Pair Potentials Across Protein Interfaces in Screening Predicted Docked Complexes. Proteins 1999, 35:364-373.
58. Chakrabarti P, Janin J: Dissecting Protein-Protein Recognition Sites. Proteins 2002, 47:334-343.
59. Sander C, Schneider R: Database of homology derived protein structures and the structural meaning of sequence alignment. Proteins 1991, 9:56-68.
60. Göbel U, Sander C, Schneider R, Valencia A: Correlated mutations and residue contacts in proteins. Proteins 1994, 18:309-317.
61. Pazos F, Helmer-Citterich M, Ausiello G, Valencia A: Correlated Mutations Contain Information About Protein-protein Interaction. J Mol Biol 1997, 271:511-523.
62. McLachlan AD: Test for comparing related amino acid sequences. Journal of Molecular Biology 1971, 61:409-424.
63. Fariselli P, Olmea O, Valencia A, Casadio R: Prediction of contact maps with neural networks and correlated mutations. Protein Engineering 2001, 14:835-843.