High-throughput identification of interacting protein-protein binding sites

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Chung, Jo Lan ^a,b   Wang, Wei ^a   Bourne, Philip E ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PARTNERS; HIGH-THROUGHPUT; MACHINE LEARNING APPROACHES; NUMBER OF METHODS; PROTEIN INTERFACES; PROTEIN-BINDING SITES; PROTEIN-PROTEIN BINDING; PUTATIVE PROTEINS;

BIOCHEMISTRY; PIPELINES;

PROTEINS;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CONTROLLED STUDY; DATA EXTRACTION; HIGH THROUGHPUT SCREENING; INFORMATION PROCESSING; MACHINE LEARNING; PREDICTION; PROTEIN DATABASE; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; ALGORITHM; ARTIFICIAL INTELLIGENCE; AUTOMATED PATTERN RECOGNITION; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; METHODOLOGY; MOLECULAR GENETICS; PROTEIN ANALYSIS; PROTEIN BINDING; SEQUENCE ANALYSIS;

AMINO ACID;

ALGORITHMS; AMINO ACID SEQUENCE; AMINO ACIDS; ARTIFICIAL INTELLIGENCE; BINDING SITES; COMPUTER SIMULATION; MODELS, CHEMICAL; MOLECULAR SEQUENCE DATA; PATTERN RECOGNITION, AUTOMATED; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; SEQUENCE ANALYSIS, PROTEIN;

EID: 34447632693     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-223     Document Type: Article

References (64)

1. von Mering C Krause R Snel B Cornell M Oliver SG Fields S Bork P Comparative assessment of large-scale data sets of protein-protein interactions Nature 2002 417 6887 399-403 10.1038/nature750 12000970
2. Fields S Song O A novel genetic system to detect protein-protein interactions Nature 1989 340 6230 245-246 10.1038/340245a0 2547163
3. McCafferty J Griffiths AD Winter G Chiswell DJ Phage antibodies: filamentous phage displaying antibody variable domains Nature 1990 348 6301 552-554 10.1038/348552a0 2247164
4. Gavin AC Bosche M Krause R Grandi P Marzioch M Bauer A Schultz J Rick JM Michon AM Cruciat CM et al. Functional organization of the yeast proteome by systematic analysis of protein complexes Nature 2002 415 6868 141-147 10.1038/415141a 11805826
5. Valencia A Pazos F Computational methods for the prediction of protein interactions Curr Opin Struct Biol 2002 12 3 368-373 10.1016/ S0959-440X(02)00333-0 12127457
6. Tamames J Casari G Ouzounis C Valencia A Conserved clusters of functionally related genes in two bacterial genomes J Mol Evol 1997 44 1 66-73 10.1007/PL00006122 9010137
7. Dandekar T Snel B Huynen M Bork P Conservation of gene order: A fingerprint of proteins that physically interact Trends Biochem Sci 1998 23 9 324-328 10.1016/S0968-0004(98)01274-2 9787636
8. Marcotte EM Pellegrini M Ng HL Rice DW Yeates TO Eisenberg D Detecting protein function and protein-protein interactions from genome sequences Science 1999 285 5428 751-753 10.1126/science.285.5428.751 10427000
9. Pellegrini M Marcotte EM Thompson MJ Eisenberg D Yeates TO Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles Proc Natl Acad Sci USA 1999 96 8 4285-4288 16324 10200254 10.1073/pnas.96.8.4285
10. Enright AJ Iliopoulos I Kyrpides NC Ouzounis CA Protein interaction maps for complete genomes based on gene fusion events Nature 1999 402 6757 86-90 10.1038/47056 10573422
11. Goh CS Bogan AA Joachimiak M Walther D Cohen FE Co-evolution of proteins with their interaction partners J Mol Biol 2000 299 2 283-293 10.1006/ jmbi.2000.3732 10860738
12. Pazos F Valencia A Similarity of phylogenetic trees as indicator of protein-protein interaction Protein Eng 2001 14 9 609-614 10.1093/ protein/14.9.609 11707606
13. Pazos F Valencia A In silico two-hybrid system for the selection of physically interacting protein pairs Proteins 2002 47 2 219-227 10.1002/ prot.10074 11933068
14. Moult J Fidelis K Zemla A Hubbard T Critical assessment of methods of protein structure prediction (CASP)-round V Proteins 2003 53 Suppl 6 334-339 10.1002/prot.10556 14579322
15. Glaser F Pupko T Paz I Bell RE Bechor-Shental D Martz E Ben-Tal N ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information Bioinformatics 2003 19 1 163-164 10.1093/bioinformatics/19.1.163 12499312
16. Landgraf R Xenarios I Eisenberg D Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins J Mol Biol 2001 307 5 1487-1502 10.1006/jmbi.2001.4540 11292355
17. Lichtarge O Bourne HR Cohen FE An evolutionary trace method defines binding surfaces common to protein families J Mol Biol 1996 257 2 342-358 10.1006/jmbi.1996.0167 8609628
18. Lichtarge O Sowa ME Evolutionary predictions of binding surfaces and interactions Curr Opin Struct Biol 2002 12 1 21-27 10.1016/ S0959-440X(02)00284-1 11839485
19. Pupko T Bell RE Mayrose I Glaser F Ben-Tal N Rate4Site: An algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues Bioinformatics 2002 18 Suppl 1 S71-77 12169533
20. Jones S Thornton JM Prediction of protein-protein interaction sites using patch analysis J Mol Biol 1997 272 1 133-143 10.1006/ jmbi.1997.1233 9299343
21. Neuvirth H Raz R Schreiber G ProMate: A structure based prediction program to identify the location of protein-protein binding sites J Mol Biol 2004 338 1 181-199 10.1016/j.jmb.2004.02.040 15050833
22. Gallet X Charloteaux B Thomas A Brasseur R A fast method to predict protein interaction sites from sequences J Mol Biol 2000 302 4 917-926 10.1006/jmbi.2000.4092 10993732
23. Chen H Zhou HX Prediction of interface residues in protein-protein complexes by a consensus neural network method: Test against NMR data Proteins 2005 61 1 21-35 10.1002/prot.20514 16080151
24. Fariselli P Pazos F Valencia A Casadio R Prediction of protein - protein interaction sites in heterocomplexes with neural networks Eur J Biochem 2002 269 5 1356-1361 10.1046/j.1432-1033.2002.02767.x 11874449
25. Ofran Y Rost B Predicted protein-protein interaction sites from local sequence information FEBS Lett 2003 544 1-3 236-239 10.1016/ S0014-5793(03)00456-3 12782323
26. Zhou HX Shan Y Prediction of protein interaction sites from sequence profile and residue neighbor list Proteins 2001 44 3 336-343 10.1002/ prot.1099 11455607
27. Bordner AJ Abagyan R Statistical analysis and prediction of protein-protein interfaces Proteins 2005 60 3 353-366 10.1002/prot.20433 15906321
28. Bradford JR Westhead DR Improved prediction of protein-protein binding sites using a support vector machines approach Bioinformatics 2005 21 8 1487-1494 10.1093/bioinformatics/bti242 15613384
29. Chung JL Wang W Bourne PE Exploiting sequence and structure homologs to identify protein-protein binding sites Proteins 2006 62 3 630-640 10.1002/prot.20741 16329107
30. Koike A Takagi T Prediction of protein-protein interaction sites using support vector machines Protein Eng Des Sel 2004 17 2 165-173 10.1093/ protein/gzh020 15047913
31. Yan C Dobbs D Honavar V A two-stage classifier for identification of protein-protein interface residues Bioinformatics 2004 20 Suppl 1 I371-I378 10.1093/bioinformatics/bth920 15262822
32. Bradford JR Needham CJ Bulpitt AJ Westhead DR Insights into protein-protein interfaces using a Bayesian network prediction method J Mol Biol 2006 362 2 365-386 10.1016/j.jmb.2006.07.028 16919296
33. 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 4 409-443 10.1002/prot.10115 12001221
34. Smith GR Sternberg MJ Prediction of protein-protein interactions by docking methods Curr Opin Struct Biol 2002 12 1 28-35 10.1016/ S0959-440X(02)00285-3 11839486
35. Aloy P Russell RB Interrogating protein interaction networks through structural biology Proc Natl Acad Sci USA 2002 99 9 5896-5901 122873 11972061 10.1073/pnas.092147999
36. Lu L Lu H Skolnick J MULTIPROSPECTOR: An algorithm for the prediction of protein-protein interactions by multimeric threading Proteins 2002 49 3 350-364 10.1002/prot.10222 12360525
37. Aloy P Bottcher B Ceulemans H Leutwein C Mellwig C Fischer S Gavin AC Bork P Superti-Furga G Serrano L et al. Structure-based assembly of protein complexes in yeast Science 2004 303 5666 2026-2029 10.1126/ science.1092645 15044803
38. Lu L Arakaki AK Lu H Skolnick J Multimeric threading-based prediction of protein-protein interactions on a genomic scale: Application to the Saccharomyces cerevisiae proteome Genome Res 2003 13 6A 1146-1154 403642 12799350 10.1101/gr.1145203
39. Vakser IA Protein-protein interfaces are special Structure 2004 12 6 910-912 10.1016/j.str.2004.05.003 15274910
40. Aloy P Ceulemans H Stark A Russell RB The relationship between sequence and interaction divergence in proteins J Mol Biol 2003 332 5 989-998 10.1016/j.jmb.2003.07.006 14499603
41. Wodak SJ Mendez R Prediction of protein-protein interactions: The CAPRI experiment, its evaluation and implications Curr Opin Struct Biol 2004 14 2 242-249 10.1016/j.sbi.2004.02.003 15093840
42. Aytuna AS Gursoy A Keskin O Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces Bioinformatics 2005 21 12 2850-2855 10.1093/bioinformatics/bti443 15855251
43. Berman HM Westbrook J Feng Z Gilliland G Bhat TN Weissig H Shindyalov IN Bourne PE The Protein Data Bank Nucleic Acids Res 2000 28 1 235-242 102472 10592235 10.1093/nar/28.1.235
44. 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 6 1027-1038 10.1016/ j.str.2004.04.009 15274922
45. Lu H Lu L Skolnick J Development of unified statistical potentials describing protein-protein interactions Biophys J 2003 84 3 1895-1901 1302758 12609891
46. Bogan AA Thorn KS Anatomy of hot spots in protein interfaces J Mol Biol 1998 280 1 1-9 10.1006/jmbi.1998.1843 9653027
47. Ansari S Helms V Statistical analysis of predominantly transient protein-protein interfaces Proteins 2005 61 2 344-355 10.1002/prot.20593 16104020
48. Glaser F Steinberg DM Vakser IA Ben-Tal N Residue frequencies and pairing preferences at protein-protein interfaces Proteins 2001 43 2 89-102 10.1002/1097-0134(20010501)43:2<89::AID-PROT1021>3.0.CO;2-H 11276079
49. Ofran Y Rost B Analysing six types of protein-protein interfaces J Mol Biol 2003 325 2 377-387 10.1016/S0022-2836(02)01223-8 12488102
50. Saha RP Bahadur RP Chakrabarti P Interresidue contacts in proteins and protein-protein interfaces and their use in characterizing the homodimeric interface J Proteome Res 2005 4 5 1600-1609 10.1021/ pr050118k 16212412
51. De S Krishnadev O Srinivasan N Rekha N Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different BMC Struct Biol 2005 5 15 1201154 16105176 10.1186/ 1472-6807-5-15
52. Pazos F Helmer-Citterich M Ausiello G Valencia A Correlated mutations contain information about protein-protein interaction J Mol Biol 1997 271 4 511-523 10.1006/jmbi.1997.1198 9281423
53. Sprinzak E Margalit H Correlated sequence-signatures as markers of protein-protein interaction J Mol Biol 2001 311 4 681-692 10.1006/ jmbi.2001.4920 11518523
54. Jones S Thornton JM Protein-protein interactions: A review of protein dimer structures Prog Biophys Mol Biol 1995 63 1 31-65 10.1016/ 0079-6107(94)00008-W 7746868
55. Zeng Z Castano AR Segelke BW Stura EA Peterson PA Wilson IA Crystal structure of mouse CD1: An MHC-like fold with a large hydrophobic binding groove Science 1997 277 5324 339-345 10.1126/ science.277.5324.339 9219685
56. Rowland P Norager S Jensen KF Larsen S Structure of dihydroorotate dehydrogenase B: Electron transfer between two flavin groups bridged by an iron-sulphur cluster Structure 2000 8 12 1227-1238 10.1016/ S0969-2126(00)00530-X 11188687
57. Card GL Knowles P Laman H Jones N McDonald NQ Crystal structure of a gamma-herpesvirus cyclin-cdk complex Embo J 2000 19 12 2877-2888 203358 10856233 10.1093/emboj/19.12.2877
58. Hopfner KP Karcher A Craig L Woo TT Carney JP Tainer JA Structural biochemistry and interaction architecture of the DNA double-strand break repair Mre11 nuclease and Rad50-ATPase Cell 2001 105 4 473-485 10.1016/ S0092-8674(01)00335-X 11371344
59. Rost B Sander C Conservation and prediction of solvent accessibility in protein families Proteins 1994 20 3 216-226 10.1002/prot.340200303 7892171
60. Kabsch W Sander C Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features Biopolymers 1983 22 12 2577-2637 10.1002/bip.360221211 6667333
61. Schölkopf B Burges CJC Smola AJ Advances in kernel methods: Support vector learning Cambridge, Mass.: MIT Press 1999
62. Bairoch A Apweiler R Wu CH Barker WC Boeckmann B Ferro S Gasteiger E Huang H Lopez R Magrane M et al. The Universal Protein Resource (UniProt) Nucleic Acids Res 2005 33 Database D154-159 540024 15608167
63. 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 Nucleic Acids Res 1997 25 17 3389-3402 146917 9254694 10.1093/ nar/25.17.3389
64. Kyte J Doolittle RF A simple method for displaying the hydropathic character of a protein J Mol Biol 1982 157 1 105-132 10.1016/ 0022-2836(82)90515-0 7108955