Prediction of Protein-Protein Interaction Sites by Random Forest Algorithm with mRMR and IFS

PLoS ONE

Volumn 7, Issue 8, 2012, Pages

  Li, Bi Qing ^b,c   Feng, Kai Yan ^d   Chen, Lei ^e   Huang, Tao ^b,c,f   Cai, Yu Dong ^a  

^a SHANGHAI UNIVERSITY   (China)

^b Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

^c SHANGHAI CENTER FOR BIOINFORMATION TECHNOLOGY   (China)

^d BGI SHENZHEN   (China)

^e SHANGHAI MARITIME UNIVERSITY   (China)

^f MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SOLVENT;

ACCURACY; AMINO ACID SEQUENCE; ANALYTIC METHOD; ANALYTICAL PARAMETERS; ARTICLE; BIOCHEMISTRY; FEATURE ANALYSIS; INCREMENTAL FEATURE SELECTION; MINIMUM REDUNDANCY MAXIMAL RELEVANCE; PHYSICAL CHEMISTRY; PREDICTIVE VALIDITY; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; RANDOM FOREST;

ALGORITHMS; COMPUTATIONAL BIOLOGY; PROTEIN CONFORMATION; PROTEINS;

EID: 84865446092     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0043927     Document Type: Article

References (54)

1. Alberts B (1989) Molecular biology of the cell: Garland Pub.
2. Gallet X, Charloteaux B, Thomas A, Brasseur R, (2000) A fast method to predict protein interaction sites from sequences. J Mol Biol 302: 917-926.
3. Ofran Y, Rost B, (2003) Predicted protein-protein interaction sites from local sequence information. FEBS Lett 544: 236-239.
4. Ofran Y, Rost B, (2007) ISIS: interaction sites identified from sequence. Bioinformatics 23: e13-16.
5. Wang B, Chen P, Huang DS, Li JJ, Lok TM, et al. (2006) Predicting protein interaction sites from residue spatial sequence profile and evolution rate. FEBS Lett 580: 380-384.
6. Zhou HX, Shan Y, (2001) Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins 44: 336-343.
7. Aytuna AS, Gursoy A, Keskin O, (2005) Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces. Bioinformatics 21: 2850-2855.
8. Neuvirth H, Raz R, Schreiber G, (2004) ProMate: a structure based prediction program to identify the location of protein-protein binding sites. J Mol Biol 338: 181-199.
9. Sikic M, Tomic S, Vlahovicek K, (2009) Prediction of protein-protein interaction sites in sequences and 3D structures by random forests. PLoS Comput Biol 5: e1000278.
10. Fariselli P, Pazos F, Valencia A, Casadio R, (2002) Prediction of protein-protein interaction sites in heterocomplexes with neural networks. Eur J Biochem 269: 1356-1361.
11. Bradford JR, Westhead DR, (2005) Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics 21: 1487-1494.
12. Koike A, Takagi T, (2004) Prediction of protein-protein interaction sites using support vector machines. Protein Eng Des Sel 17: 165-173.
13. Li N, Sun Z, Jiang F, (2008) Prediction of protein-protein binding site by using core interface residue and support vector machine. BMC Bioinformatics 9: 553.
14. Bradford JR, Needham CJ, Bulpitt AJ, Westhead DR, (2006) Insights into protein-protein interfaces using a Bayesian network prediction method. J Mol Biol 362: 365-386.
15. Bernardes JS, Fernandez JH, Vasconcelos AT, (2008) Structural descriptor database: a new tool for sequence-based functional site prediction. BMC Bioinformatics 9: 492.
16. Li MH, Lin L, Wang XL, Liu T, (2007) Protein-protein interaction site prediction based on conditional random fields. Bioinformatics 23: 597-604.
17. Chen XW, Jeong JC, (2009) Sequence-based prediction of protein interaction sites with an integrative method. Bioinformatics 25: 585-591.
18. Nguyen MN, Rajapakse JC, (2006) Protein-Protein Interface Residue Prediction with SVM Using Evolutionary Profiles and Accessible Surface Areas; 28-29 Sept. 2006: 1-5.
19. Stein A, Ceol A, Aloy P, (2011) 3did: identification and classification of domain-based interactions of known three-dimensional structure. Nucleic Acids Res 39: D718-723.
20. Li W, Godzik A, (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658-1659.
21. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
22. Kawashima S, Kanehisa M, (2000) AAindex: amino acid index database. Nucleic Acids Res 28: 374.
23. Atchley WR, Zhao J, Fernandes AD, Druke T, (2005) Solving the protein sequence metric problem. Proc Natl Acad Sci U S A 102: 6395-6400.
24. Wright PE, Dyson HJ, (1999) Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. Journal of Molecular Biology 293: 321-331.
25. Dunker AK, Brown CJ, Lawson JD, Iakoucheva LM, Obradovic Z, (2002) Intrinsic disorder and protein function. Biochemistry 41: 6573-6582.
26. Liu J, Tan H, Rost B, (2002) Loopy proteins appear conserved in evolution. Journal of Molecular Biology 322: 53-64.
27. Tompa P, (2002) Intrinsically unstructured proteins. Trends in Biochemical Sciences 27: 527-533.
28. Peng K, Radivojac P, Vucetic S, Dunker AK, Obradovic Z, (2006) Length-dependent prediction of protein intrinsic disorder. BMC Bioinformatics 7: 208.
29. Cheng J, Randall AZ, Sweredoski MJ, Baldi P, (2005) SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Research 33: W72-W76.
30. Hoskins J, Lovell S, Blundell TL, (2006) An algorithm for predicting protein-protein interaction sites: Abnormally exposed amino acid residues and secondary structure elements. Protein Sci 15: 1017-1029.
31. Jones S, Thornton JM, (1997) Analysis of protein-protein interaction sites using surface patches. J Mol Biol 272: 121-132.
32. Mihel J, Sikic M, Tomic S, Jeren B, Vlahovicek K, (2008) PSAIA- protein structure and interaction analyzer. BMC Struct Biol 8: 21.
33. Tsodikov OV, Record MT Jr, Sergeev YV, (2002) Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature. J Comput Chem 23: 600-609.
34. Peng H, Long F, Ding C, (2005) Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy. IEEE Trans Pattern Anal Mach Intell 27: 1226-1238.
35. Breiman L, (2001) Random forests. Machine learning 45: 5-32.
36. Kohavi R (1995) A Study of Cross-Validation and Bootstrap for Accuracy Estimation and Model Selection; San Mateo. 1137-1143.
37. Baldi P, Brunak S, Chauvin Y, Andersen C, Nielsen H, (2000) Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 16: 412-424.
38. Bunescu R, Ge R, Kate RJ, Marcotte EM, Mooney RJ, et al. (2005) Comparative experiments on learning information extractors for proteins and their interactions. Artificial Intelligence in Medicine 33: 139-155.
39. Davis J, Goadrich M (2006) The relationship between Precision-Recall and ROC curves. ICML '06 Proceedings of the 23rd international conference on Machine learning. 233-240. doi: 10.1145/1143844.1143874.
40. Li B-Q, Hu L-L, Chen L, Feng K-Y, Cai Y-D, et al. (2012) Prediction of Protein Domain with mRMR Feature Selection and Analysis. PLoS One 7: e39308.
41. Li BQ, Hu LL, Niu S, Cai YD, Chou KC, (2012) Predict and analyze S-nitrosylation modification sites with the mRMR and IFS approaches. J Proteomics 75: 1654-1665.
42. Kini RM, Evans HJ, (1995) A hypothetical structural role for proline residues in the flanking segments of protein-protein interaction sites. Biochem Biophys Res Commun 212: 1115-1124.
43. Stewart DE, Sarkar A, Wampler JE, (1990) Occurrence and role of cis peptide bonds in protein structures. J Mol Biol 214: 253-260.
44. Chou PY, Fasman GD, (1978) Prediction of the secondary structure of proteins from their amino acid sequence. Adv Enzymol Relat Areas Mol Biol 47: 45-148.
45. Talavera D, Robertson DL, Lovell SC, (2011) Characterization of Protein-Protein Interaction Interfaces from a Single Species. PLoS One 6: e21053.
46. Guharoy M, Chakrabarti P, (2007) Secondary structure based analysis and classification of biological interfaces: identification of binding motifs in protein-protein interactions. Bioinformatics 23: 1909-1918.
47. Jian-Tao Y, Mao-Zu G, (2008) Prediction of Protein-Protein Interactions from Secondary Structures in Binding Motifs Using the Statistic Method; 18-20 Oct. 2008: 100-103.
48. Moreira IS, Fernandes PA, Ramos MJ, (2007) Hot spots-a review of the protein-protein interface determinant amino-acid residues. Proteins 68: 803-812.
49. Xia JF, Zhao XM, Song J, Huang DS, (2010) APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility. BMC Bioinformatics 11: 174.
50. Monji H, Koizumi S, Ozaki T, Ohkawa T, (2011) Interaction site prediction by structural similarity to neighboring clusters in protein-protein interaction networks. BMC Bioinformatics 12 (Suppl 1):: S39.
51. Laskowski RA (1995) SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J Mol Graph 13: 323-330, 307-328.
52. Dundas J, Ouyang Z, Tseng J, Binkowski A, Turpaz Y, et al. (2006) CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res 34: W116-118.
53. Zhou W, Yan H, (2011) Prediction of DNA-binding protein based on statistical and geometric features and support vector machines. Proteome Science 9: S1.
54. Grabe M, Neu J, Oster G, Nollert P, (2003) Protein interactions and membrane geometry. Biophys J 84: 854-868.