Protein-protein interaction site predictions with three-dimensional probability distributions of interacting atoms on protein surfaces

PLoS ONE

Volumn 7, Issue 6, 2012, Pages

  Chen, Ching Tai ^a,d,e   Peng, Hung Pin ^a,b,e   Jian, Jhih Wei ^a,b,e   Tsai, Keng Chang ^a   Chang, Jeng Yih ^a   Yang, Ei Wen ^a,e   Chen, Jun Bo ^a,c   Ho, Shinn Ying ^d   Hsu, Wen Lian ^e   Yang, An Suei ^a  

^a GENOMICS RESEARCH CENTER   (Taiwan)

^b NATIONAL YANG MING UNIVERSITY   (Taiwan)

^c NATIONAL TSING HUA UNIVERSITY   (Taiwan)

^d NATIONAL CHIAO TUNG UNIVERSITY   (Taiwan)

^e INSTITUTE OF INFORMATION SCIENCE   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; PROTEIN;

ACCURACY; ALGORITHM; AMINO ACID COMPOSITION; ARTICLE; ATOM; CONTROLLED STUDY; COVALENT BOND; HYDROPHOBICITY; MACHINE LEARNING; MOLECULAR MODEL; PHYSICAL CHEMISTRY; PREDICTION; PROBABILITY; PROTEIN DATABASE; PROTEIN PROTEIN INTERACTION; SENSITIVITY AND SPECIFICITY; SIMULATION; SURFACE PROPERTY; VALIDATION PROCESS; ARTIFICIAL INTELLIGENCE; ARTIFICIAL NEURAL NETWORK; BIOLOGY; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; METHODOLOGY; NONPARAMETRIC TEST; PROTEIN ANALYSIS; STATISTICAL DISTRIBUTION;

ALGORITHMS; AMINO ACIDS; ARTIFICIAL INTELLIGENCE; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; MODELS, CHEMICAL; MODELS, MOLECULAR; NEURAL NETWORKS (COMPUTER); PROBABILITY; PROTEIN INTERACTION MAPPING; PROTEINS; STATISTICAL DISTRIBUTIONS; STATISTICS, NONPARAMETRIC;

EID: 84862003258     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0037706     Document Type: Article

References (55)

1. Wass MN, David A, Sternberg MJ, (2011) Challenges for the prediction of macromolecular interactions. Curr Opin Struct Biol 21: 382-390.
2. Tuncbag N, Gursoy A, Keskin O, (2011) Prediction of protein-protein interactions: unifying evolution and structure at protein interfaces. Phys Biol 8: 035006.
3. Ezkurdia I, Bartoli L, Fariselli P, Casadio R, Valencia A, et al. (2009) Progress and challenges in predicting protein-protein interaction sites. Brief Bioinform 10: 233-246.
4. Keskin O, Gursoy A, Ma B, Nussinov R, (2008) Principles of protein-protein interactions: what are the preferred ways for proteins to interact? Chem Rev 108: 1225-1244.
5. de Vries SJ, Bonvin AM, (2008) How proteins get in touch: interface prediction in the study of biomolecular complexes. Curr Protein Pept Sci 9: 394-406.
6. Zhou HX, Qin S, (2007) Interaction-site prediction for protein complexes: a critical assessment. Bioinformatics 23: 2203-2209.
7. Janin J, Bahadur RP, Chakrabarti P, (2008) Protein-protein interaction and quaternary structure. Q Rev Biophys 41: 133-180.
8. Chakrabarti P, Janin J, (2002) Dissecting protein-protein recognition sites. Proteins 47: 334-343.
9. Lo Conte L, Chothia C, Janin J, (1999) The atomic structure of protein-protein recognition sites. J Mol Biol 285: 2177-2198.
10. Levy ED, (2010) A simple definition of structural regions in proteins and its use in analyzing interface evolution. J Mol Biol 403: 660-670.
11. Glaser F, Steinberg DM, Vakser IA, Ben-Tal N, (2001) Residue frequencies and pairing preferences at protein-protein interfaces. Proteins 43: 89-102.
12. Moreira IS, Fernandes PA, Ramos MJ, (2007) Hot spots-a review of the protein-protein interface determinant amino-acid residues. Proteins 68: 803-812.
13. Bogan AA, Thorn KS, (1998) Anatomy of hot spots in protein interfaces. J Mol Biol 280: 1-9.
14. Rodier F, Bahadur RP, Chakrabarti P, Janin J, (2005) Hydration of protein-protein interfaces. Proteins 60: 36-45.
15. Ofran Y, Rost B, (2003) Analysing six types of protein-protein interfaces. J Mol Biol 325: 377-387.
16. Ofran Y, Rost B, (2007) ISIS: interaction sites identified from sequence. Bioinformatics 23: e13-16.
17. Res I, Mihalek I, Lichtarge O, (2005) An evolution based classifier for prediction of protein interfaces without using protein structures. Bioinformatics 21: 2496-2501.
18. Koike A, Takagi T, (2004) Prediction of protein-protein interaction sites using support vector machines. Protein Eng Des Sel 17: 165-173.
19. Ofran Y, Rost B, (2003) Predicted protein-protein interaction sites from local sequence information. FEBS Lett 544: 236-239.
20. 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.
21. Chang DT, Syu YT, Lin PC, (2010) Predicting the protein-protein interactions using primary structures with predicted protein surface. BMC Bioinformatics 11 (Suppl 1): S3.
22. Murakami Y, Mizuguchi K, (2010) Applying the Naive Bayes classifier with kernel density estimation to the prediction of protein-protein interaction sites. Bioinformatics 26: 1841-1848.
23. Li MH, Lin L, Wang XL, Liu T, (2007) Protein-protein interaction site prediction based on conditional random fields. Bioinformatics 23: 597-604.
24. 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.
25. Engelen S, Trojan LA, Sacquin-Mora S, Lavery R, Carbone A, (2009) Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling. PLoS Comput Biol 5: e1000267.
26. 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.
27. Porollo A, Meller J, (2007) Prediction-based fingerprints of protein-protein interactions. Proteins 66: 630-645.
28. Zhang QC, Petrey D, Norel R, Honig BH, (2010) Protein interface conservation across structure space. Proc Natl Acad Sci U S A 107: 10896-10901.
29. Murakami Y, Jones S, (2006) SHARP2: protein-protein interaction predictions using patch analysis. Bioinformatics 22: 1794-1795.
30. Negi SS, Braun W, (2007) Statistical analysis of physical-chemical properties and prediction of protein-protein interfaces. J Mol Model 13: 1157-1167.
31. Kufareva I, Budagyan L, Raush E, Totrov M, Abagyan R, (2007) PIER: protein interface recognition for structural proteomics. Proteins 67: 400-417.
32. Sacquin-Mora S, Carbone A, Lavery R, (2008) Identification of Protein Interaction Partners and Protein-Protein Interaction Sites. Journal of Molecular Biology 382: 1276-1289.
33. Wass MN, Fuentes G, Pons C, Pazos F, Valencia A, (2011) Towards the prediction of protein interaction partners using physical docking. Mol Syst Biol 7: 469.
34. Kundrotas PJ, Vakser IA, (2010) Accuracy of protein-protein binding sites in high-throughput template-based modeling. PLoS Comput Biol 6: e1000727.
35. Chen CT, Yang EW, Hsu HJ, Sun YK, Hsu WL, et al. (2008) Protease substrate site predictors derived from machine learning on multilevel substrate phage display data. Bioinformatics 24: 2691-2697.
36. Sheinerman FB, Norel R, Honig B, (2000) Electrostatic aspects of protein-protein interactions. Curr Opin Struct Biol 10: 153-159.
37. Moont G, Gabb HA, Sternberg MJ, (1999) Use of pair potentials across protein interfaces in screening predicted docked complexes. Proteins 35: 364-373.
38. Jones S, Thornton JM, (1996) Principles of protein-protein interactions. Proc Natl Acad Sci U S A 93: 13-20.
39. Zhang QC, Deng L, Fisher M, Guan J, Honig B, et al. (2011) PredUs: a web server for predicting protein interfaces using structural neighbors. Nucleic Acids Res 39: W283-287.
40. Jiang L, Kuhlman B, Kortemme T, Baker D, (2005) A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces. Proteins 58: 893-904.
41. Yu CM, Peng HP, Chen IC, Lee YC, Chen JB, et al. (2012) Rationalization and design of the complementarity determining region sequences in an antibody-antigen recognition interface. PLoS One 7: e33340.
42. McConkey BJ, Sobolev V, Edelman M, (2003) Discrimination of native protein structures using atom-atom contact scoring. Proceedings of the National Academy of Sciences of the United States of America 100: 3215-3220.
43. Elkins JM, Ryle MJ, Clifton IJ, Dunning Hotopp JC, Lloyd JS, et al. (2002) X-ray crystal structure of Escherichia coli taurine/alpha-ketoglutarate dioxygenase complexed to ferrous iron and substrates. Biochemistry 41: 5185-5192.
44. Henrick K, Thornton JM, (1998) PQS: a protein quaternary structure file server. Trends Biochem Sci 23: 358-361.
45. Hubbard SJ, Thornton JM, (1993) NACCESS: Department of Biochemistry and Molecular Biology, University College London. Software available athttp://www.bioinf.manchester.ac.uk/naccess/nacdownload.html.
46. Rumelhart DE, Hinton GE, Williams RJ, (1986) Learning internal representations by error propagation: MIT Press pp. 318-362.
47. Levenberg K, (1944) A Method for the Solution of Certain Non-Linear Problems in Least Squares. The Quarterly of Applied Mathematics 2: 164-168.
48. Reidmiller M, Braun H, (1993) A direct adaptive method for faster backpropagation learning: the RPROP algorithm. IEEE Int Conf Neural Networks pp. 586-591.
49. Riedmiller M, (1994) Rprop-Description and Implementation Details Technical Report. University of Karlsruhe.
50. Burges CJC, (1998) A tutorial on Support Vector Machines for pattern recognition. Data Mining and Knowledge Discovery 2: 121-167.
51. Chang CC, Lin CJ, (2001) LIBSVM: A library for support vector machines. pp. Software available athttp://www.csie.ntu.edu.tw/~cjlin/libsvm.
52. Breiman L, (1996) Bagging predictors. Machine Learning 24: 123-140.
53. Manning CD, Raghavan P, Schutze H, (2007) An introduction to information retrieval. Cambridge, England Cambridge University Press.
54. Matthews BW, (1975) Comparison of Predicted and Observed Secondary Structure of T4 Phage Lysozyme. Biochimica Et Biophysica Acta 405: 442-451.
55. Laskowski RA, Thornton JM, Humblet C, Singh J, (1996) X-SITE: use of empirically derived atomic packing preferences to identify favourable interaction regions in the binding sites of proteins. J Mol Biol 259: 175-201.