Prediction of protein interaction sites

Computational Protein-Protein Interactions

Volumn , Issue , 2009, Pages 167-184

  Ofran, Yanay ^a  

^a BAR ILAN UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84994239100     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1201/9781420070071     Document Type: Chapter

References (83)

1. Archakov, A. I., V. M. Govorun, et al. (2003). “Protein-protein interactions as a target for drugs in proteomics.” Proteomics 3(4): 380-91.
2. Arkin, M. R. and J. A. Wells (2004). “Small-molecule inhibitors of protein-protein interactions: Progressing towards the dream.” Nat Rev Drug Discov 3(4): 301-17.
3. Armon, A., D. Graur, et al. (2001). “ConSurf: An algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information.” J Mol Biol 307(1): 447-63.
4. Bahadur, R. P., P. Chakrabarti, et al. (2004). “A dissection of specific and non-specific protein-protein interfaces.” J Mol Biol 336(4): 943-55.
5. Baldi, P., S. Brunak, et al. (2000). “Assessing the accuracy of prediction algorithms for classification: An overview.” Bioinformatics 16(5): 412-24.
6. Balter, M. (1998). “Revealing HIV’s T cell passkey.” Science 280(5371): 1833-4.
7. Blythe, M. J. and D. R. Flower (2005). “Benchmarking B cell epitope prediction: Underperformance of existing methods.” Protein Sci 14(1): 246-8.
8. Bogan, A. A. and K. S. Thorn (1998). “Anatomy of hot spots in protein interfaces.” J Mol Biol 280(1): 1-9.
9. Bordner, A. J. and R. Abagyan (2005). “Statistical analysis and prediction of protein-protein interfaces.” Proteins 60(3): 353-66.
10. Bradford, J. R., C. J. Needham, et al. (2006). “Insights into protein-protein interfaces using a Bayesian network prediction method.” J Mol Biol 362(2): 365-86.
11. Bradford, J. R. and D. R. Westhead (2005). “Improved prediction of protein-protein binding sites using a support vector machines approach.” Bioinformatics 21(8): 1487-94.
12. Burgoyne, N. J. and R. M. Jackson (2006). “Predicting protein interaction sites: Binding hot-spots in protein-protein and protein-ligand interfaces.” Bioinformatics 22(11): 1335-42.
13. Caffrey, D. R., S. Somaroo, et al. (2004). “Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?” Protein Sci 13(1): 190-202.
14. Chen, H. and H. X. Zhou (2005). “Prediction of interface residues in protein-protein complexes by a consensus neural network method: Test against NMR data.” Proteins 61(1): 21-35.
15. Chung, J. L., W. Wang, et al. (2006). “Exploiting sequence and structure homologs to identify protein-protein binding sites.” Proteins 62(3): 630-40.
16. Clackson, T. and J. A. Wells (1995). “A hot spot of binding energy in a hormone-receptor interface.” Science 267(5196): 383-6.
17. Darnell, S. J., L. LeGault, et al. (2008). “KFC Server: Interactive forecasting of protein interaction hot spots.” Nucleic Acids Res 36(Web Server issue): W265-9.
18. de Vries, S. J. and A. M. Bonvin (2008). “How proteins get in touch: Interface prediction in the study of biomolecular complexes.” Curr Protein Pept Sci 9(4): 394-406.
19. de Vries, S. J., A. D. van Dijk, et al. (2006). “WHISCY: What information does surface conservation yield? Application to data-driven docking.” Proteins 63(3): 479-89.
20. Dong, Q., X. Wang, et al. (2007). “Exploiting residue-level and profile-level interface propensities for usage in binding sites prediction of proteins.” BMC Bioinformatics 8: 147.
21. Fariselli, P., F. Pazos, et al. (2002). “Prediction of protein-protein interaction sites in heterocomplexes with neural networks.” Eur J Biochem 269(5): 1356-61.
22. Fernandez-Recio, J., M. Totrov, et al. (2004). “Identification of protein-protein interaction sites from docking energy landscapes.” J Mol Biol 335(3): 843-65.
23. Gallet, X., B. Charloteaux, et al. (2000). “A fast method to predict protein interaction sites from sequences.” J Mol Biol 302(4): 917-26.
24. Glaser, F., D. M. Steinberg, et al. (2001). “Residue frequencies and pairing pReferences at protein-protein interfaces.” Proteins 43(2): 89-102.
25. Greenbaum, J. A., P. H. Andersen, et al. (2007). “Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools.” J Mol Recognit 20(2): 75-82.
26. Guney, E., N. Tuncbag, et al. (2008). “HotSprint: Database of computational hot spots in protein interfaces.” Nucleic Acids Res 36(Database issue): D662-6.
27. Guo, J., X. Wu, et al. (2008). “Genome-wide inference of protein interaction sites: Lessons from the yeast high-quality negative protein-protein interaction dataset.” Nucleic Acids Res 36(6): 2002-11.
28. Halperin, I., H. Wolfson, et al. (2004). “Protein-protein interactions; coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking.” Structure 12(6): 1027-38.
29. Haste Andersen, P., M. Nielsen, et al. (2006). “Prediction of residues in discontinuous B-cell epitopes using protein 3D structures.” Protein Sci 15(11): 2558-67.
30. Jackson, R. M. (1999). “Comparison of protein-protein interactions in serine protease-inhibitor and antibody-antigen complexes: Implications for the protein docking problem.” Protein Sci 8(3): 603-13.
31. Janin, J. (1995). “Protein-protein recognition.” Progress in Biophysics and Molecular Biology 21: 145-66.
32. Jones, S. and J. M. Thornton (1996). “Principles of protein-protein interactions.” Proc Natl Acad Sci USA 93(1): 13-20.
33. Jones, S. and J. M. Thornton (1997). “Prediction of protein-protein interaction sites using patch analysis.” Journal of Molecular Biology 272(1): 133-43.
34. Kabat, E. A. (1985). Immunoglobulin sequence data. The generation of antibody diversity and its genetic control. In The Role of Data in Scientific Progress, edited by P. S. Glaeser, pp. 97-102. North Holland: Elsevier.
35. Kerrien, S., Y. Alam-Faruque, et al. (2007). “IntAct: Open source resource for molecular interaction data.” Nucleic Acids Res 35(Database issue): D561-5.
36. Keskin, O., I. Bahar, et al. (1998). “Empirical solvent-mediated potentials hold for both intramolecular and inter-molecular inter-residue interactions.” Protein Sci 7(12): 2578-86.
37. Keskin, O., C. J. Tsai, et al. (2004). “A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications.” Protein Sci 13(4): 1043-55.
38. Kini, R. M. and H. J. Evans (1996). “Prediction of potential protein-protein interaction sites from amino acid sequence. Identification of a fibrin polymerization site.” FEBS Lett 385(1-2): 81-86.
39. Koblish, H. K., S. Zhao, et al. (2006). “Benzodiazepinedione inhibitors of the Hdm2:p53 complex suppress human tumor cell proliferation in vitro and sensitize tumors to doxorubicin in vivo.” Mol Cancer Ther 5(1): 160-9.
40. Koike, A. and T. Takagi (2004). “Prediction of protein-protein interaction sites using support vector machines.” Protein Eng Des Sel 17(2): 165-73.
41. Kortemme, T. and D. Baker (2002). “A simple physical model for binding energy hot spots in protein-protein complexes.” Proc Natl Acad Sci USA 99(22): 14116-21.
42. Kufareva, I., L. Budagyan, et al. (2007). “PIER: Protein interface recognition for structural proteomics.” Proteins 67(2): 400-17.
43. Kwong, P. D., R. Wyatt, et al. (1998). “Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody.” Nature 393(6686): 648-59.
44. Laskowski, R. A., N. M. Luscombe, et al. (1996). “Protein clefts in molecular recognition and function.” Protein Sci 5(12): 2438-52.
45. Li, J. J., D. S. Huang, et al. (2006). “Identifying protein-protein interfacial residues in heterocomplexes using residue conservation scores.” Int J Biol Macromol 38(3-5): 241-7.
46. Liang, S., C. Zhang, et al. (2006). “Protein binding site prediction using an empirical scoring function.” Nucleic Acids Res 34(13): 3698-707.
47. Lo Conte, L., C. Chothia, et al. (1999). “The atomic structure of protein-protein recognition sites.” J Mol Biol 285(5): 2177-98.
48. Ma, B., T. Elkayam, et al. (2003). “Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces.” Proc Natl Acad Sci USA 100(10): 5772-7.
49. Ma, B., H. J. Wolfson, et al. (2001). “Protein functional epitopes: Hot spots, dynamics and combinatorial libraries.” Curr Opin Struct Biol 11(3): 364-9.
50. McCoy, A. J., V. Chandana Epa, et al. (1997). “Electrostatic complementarity at protein/protein interfaces.” J Mol Biol 268(2): 570-84.
51. Mika, S. and B. Rost (2006). “Protein-protein interactions more conserved within species than across species.” PLoS Comput Biol 2(7): e79.
52. Morrison, K. L. and G. A. Weiss (2001). “Combinatorial alanine-scanning.” Curr Opin Chem Biol 5(3): 302-7.
53. Murga, L. F., M. J. Ondrechen, et al. (2008). “Prediction of interaction sites from apo 3D structures when the holo conformation is different.” Proteins 72(3): 980-92.
54. Negi, S. S., C. H. Schein, et al. (2007). “InterProSurf: A web server for predicting interacting sites on protein surfaces.” Bioinformatics 23(24): 3397-9.
55. Neuvirth, H., U. Heinemann, et al. (2007). “ProMateus—an open research approach to protein- binding sites analysis.” Nucleic Acids Res 35(Web Server issue): W543-8.
56. Neuvirth, H., R. Raz, et al. (2004). “ProMate: A structure based prediction program to identify the location of protein-protein binding sites.” J Mol Biol 338(1): 181-99.
57. Ofran, Y. and B. Rost (2003a). “Analysing six types of protein-protein interfaces.” J Mol Biol 325(2): 377-87.
58. Ofran, Y. and B. Rost (2003b). “Predicted protein-protein interaction sites from local sequence information.” FEBS Lett 544(1-3): 236-9.
59. Ofran, Y. and B. Rost (2007a). “ISIS: Interaction sites identified from sequence.” Bioinformatics 23(2): e13-6.
60. Ofran, Y. and B. Rost (2007b). “Protein-protein interaction hotspots carved into sequences.” PLoS Comput Biol 3(7): e119.
61. Ofran, Y., A. Schlessinger, et al. (2008). “Automated identification of complementarity determining regions reveals peculiar characteristics of CDRs and B-Cell epitopes.” J Immunol 181: 6230-35.
62. Pazos, F. and A. Valencia (2002). “In silico two-hybrid system for the selection of physically interacting protein pairs.” Proteins 47(2): 219-27.
63. Peters, K. P., J. Fauck, et al. (1996). “The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria.” J Mol Biol 256(1): 201-13.
64. Pettit, F. K., E. Bare, et al. (2007). “HotPatch: A statistical approach to finding biologically relevant features on protein surfaces.” J Mol Biol 369(3): 863-79.
65. Pettit, F. K. and J. U. Bowie (1999). “Protein surface roughness and small molecular binding sites.” J Mol Biol 285(4): 1377-82.
66. Qin, S. and H. X. Zhou (2007). “meta-PPISP: A meta web server for protein-protein interaction site prediction.” Bioinformatics 23(24): 3386-7.
67. Res, I., I. Mihalek, et al. (2005). “An evolution based classifier for prediction of protein interfaces without using protein structures.” Bioinformatics 21(10): 2496-501.
68. Rost, B. (1999). “Twilight zone of protein sequence alignments.” Protein Eng 12(2): 85-94.
69. Rost, B., J. Liu, et al. (2003). “Automatic prediction of protein function.” Cell Mol Life Sci 60(12): 2637-50.
70. Rudolph, J. (2007). “Inhibiting transient protein-protein interactions: Lessons from the Cdc25 protein tyrosine phosphatases.” Nat Rev Cancer 7(3): 202-11.
71. Sheinerman, F. B., R. Norel, et al. (2000). “Electrostatic aspects of protein-protein interactions.” Curr Opin Struct Biol 10(2): 153-9.
72. Smith, G. R. and M. J. Sternberg (2002). “Prediction of protein-protein interactions by docking methods.” Curr Opin Struct Biol 12(1): 28-35.
73. Sprinzak, E., Y. Altuvia, et al. (2006). “Characterization and prediction of protein-protein interactions within and between complexes.” Proc Natl Acad Sci USA 103(40): 14718-23.
74. Sprinzak, E. and H. Margalit (2001). “Correlated sequence-signatures as markers of protein-protein interaction.” J Mol Biol 311(4): 681-92.
75. Thorn, K. S. and A. A. Bogan (2001). “ASEdb: A database of alanine mutations and their effects on the free energy of binding in protein interactions.” Bioinformatics 17(3): 284-5.
76. Vassilev, L. T. (2004). “Small-molecule antagonists of p53-MDM2 binding: Research tools and potential therapeutics.” Cell Cycle 3(4): 419-21.
77. Vassilev, L. T., B. T. Vu, et al. (2004). “In vivo activation of the p53 pathway by small-molecule antagonists of MDM2.” Science 303(5659): 844-8.
78. Wang, B., P. Chen, et al. (2006). “Predicting protein interaction sites from residue spatial sequence profile and evolution rate.” FEBS Lett 580(2): 380-4.
79. Wang, B., H. S. Wong, et al. (2006). “Inferring protein-protein interacting sites using residue conservation and evolutionary information.” Protein Pept Lett 13(10): 999-1005.
80. Wells, J. A. (1991). “Systematic mutational analyses of protein-protein interfaces.” Methods Enzymol 202: 390-411.
81. Wells, J. A. and C. L. McClendon (2007). “Reaching for high-hanging fruit in drug discovery at protein-protein interfaces.” Nature 450(7172): 1001-9.
82. Yan, C., V. Honavar, et al. (2004). “Identification of interface residues in protease-inhibitor and antigen-antibody complexes: A support vector machine approach.” Neural Computing & Applications 13(3): 123-129.
83. Zhou, H. X. and S. Qin (2007). “Interaction-site prediction for protein complexes: A critical assessment.” Bioinformatics 23(17): 2203-9.