Improving predictions of protein-protein interfaces by combining amino acid-specific classifiers based on structural and physicochemical descriptors with their weighted neighbor averages

PLoS ONE

Volumn 9, Issue 1, 2014, Pages

  De Moraes, Fábio R ^a,b   Neshich, Izabella A P ^a,b   Mazoni, Ivan ^a,b   Yano, Inácio H ^b   Pereira, José G C ^a,b   Salim, José A ^a   Jardine, José G ^b   Neshich, Goran ^b  

^a UNIVERSITY OF CAMPINAS   (Brazil)

^b EMBRAPA CERRADOS   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLASSIFIER; COMPUTER PROGRAM; CONTROLLED STUDY; DATA BASE; FALSE POSITIVE RESULT; INTERMETHOD COMPARISON; MEASUREMENT ACCURACY; PHYSICAL CHEMISTRY; PREDICTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; RECEIVER OPERATING CHARACTERISTIC; SENSITIVITY ANALYSIS;

ALGORITHMS; AMINO ACIDS; BINDING SITES; COMPUTATIONAL BIOLOGY; CYSTEINE; PRINCIPAL COMPONENT ANALYSIS; PROTEIN INTERACTION MAPS; PROTEIN STRUCTURE, TERTIARY;

EID: 84900332705     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0087107     Document Type: Article

References (61)

1. Reichmann D, Rahat O, Cohen M, Neuvirth H, Schreiber G (2007) The Molecular Architecture of protein-protein binding sites. Curr Opin Struct Biol, 17:67-76. (Pubitemid 46240815)
2. 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.
3. Xenarios I, Eisenberg D (2001) Protein interaction databases. Curr Opin Biotech, 12:334-339. (Pubitemid 32718785)
4. Chen H, Skolnick J (2008) M-TASSER: An algorithm for protein quaternary structure prediction. Biophysical Journal, 94: 918-928. (Pubitemid 351162458)
5. Jones S, Thornton JM (1996) Principles of protein-protein interactions. Proc. Natl. Acad. Sci., 93: 13-20. (Pubitemid 26038096)
6. Brinda KV, Vishveshwara S (2005) Oligomeric Protein Structure Networks: Insight into protein protein interactions. BMC Bioinformatics, 6: 296-310.
7. Ponstingl H, Kabir T, Gorse D, Thornton JM (2005) Morphological aspects of oligomeric protein structures. Progress in Biophysics and Molecular Biology, 89: 9-35. (Pubitemid 40483213)
8. Tsuchiya Y, Kinoshita K, Nakamura H (2006) Analyses of homo-oligomer interfaces of proteins from the complementarity of molecular surface, electrostatic potential and hydrophobicity. Protein Engineering, Design & Selection, 19: 421-429. (Pubitemid 44306060)
9. 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., 338:181-99. (Pubitemid 38429796)
10. Neshich G, Borro LC, Higa RH, Kuser PR, Yamagishi ME, et al. (2005) The Diamond STING server. Nucleic Acids Res., 33(2):W29-W35. (Pubitemid 44529875)
11. Neshich G, Mancini AL, Yamagishi ME, Kuser PR, Fileto R, et al. (2005) STING report: convenient web-based application for graphic and tabular presentations of protein sequence, structure and function descriptors from the STING database. Nucleic Acids Res., 33:D269-D274. (Pubitemid 40207876)
12. Mancini AL, Higa RH, Oliveira A, Dominiquini F, Kuser PR, et al. (2004) STING Contacts: a web-based application for identification and analysis of amino acid contacts within protein structure and across protein interfaces. Bioinformatics, 20(13):2145-2147. (Pubitemid 39236570)
13. Neshich G, Mazoni I, Oliveira SR, Yamagishi ME, Kuser-Falcão PR, et al. (2006) The Star STING server: a multiplatform environment for protein structure analysis. Genet. Mol. Res., 5(4): 717-722. (Pubitemid 44904629)
14. Borro LC, Oliveira SR, Yamagishi ME, Mancini AL, Jardine JG, et al. (2006) Predicting enzyme class from protein structure using Bayesian classification. Genet. Mol. Res., 5: 193-202.
15. Fernandez JH, Hayashi MA, Camargo AC, Neshich G (2003) Structural basis of the lisinopril-binding specificity in N- and C-domains of human somatic ACE. Biochem. and Biophys. Res. Comm., 308(2):219-226.
16. de Freitas SM, de Mello LV, da Silva MC, Vriend G, Neshich G, et al. (1997) Analysis of the black-eyed pea trypsin and chymotrypsin inhibitor alpha-chymotrypsin complex. FEBS Letters, 409(2):121-127.
17. Marcellino LH, Neshich G, Grossi de Sá MF, Krebbers E, Gander ES (1996) Modified 2S albumins with improved tryptophan content are correctly expressed in transgenic tobacco plants. FEBS Letters, 385(3):154-158. (Pubitemid 26167450)
18. Simões M, Bahia D, Zerlotini A, Torres K, Artiguenave F, et al. (2007) Single nucleotide polymorphisms identification in expressed genes of Schistosoma mansoni. Mol. Biochem. Parasitology, 154(2):134-140.
19. Melo RC, Ribeiro C, Murray CS, Veloso CJ, da Silveira CH, et al. (2007) Finding protein-protein interaction patterns by contact map matching. Genet. Mol. Res. 6(4):946-963. (Pubitemid 350292806)
20. Higa RH, Montagner AJ, Togawa RC, Kuser PR, Yamagishi ME, et al. (2004) ConSSeq: a web-based application for analysis of amino acid conservation based on HSSP database and within context of structure. Bioinformatics, 20(12):1983-1985. (Pubitemid 39199067)
21. Radzicka A, Wolfenden R (1988) Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution. Biochemistry, 27: 1664-1670.
22. Liang S, Zhang C, Liu S, Zhou Y (2006) Protein binding site prediction using an empirical scoring function. Nucleic Acids Res., 34(13):3698-707. (Pubitemid 44400419)
23. Porollo A, Meller J (2007) Prediction-based fingerprints of protein-protein interactions. Proteins, 66:630-45. (Pubitemid 46106767)
24. Zhou HX, Qin S (2007) Interaction-site prediction for protein complexes: a critical assessment. Bioinformatics, 23(17):2203-2209.
25. Bradford JR, Westhead DR (2005) Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics; 21:1487-1494. (Pubitemid 40542704)
26. Chen H, Zhou H-X (2005) Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data. Proteins, 61:21-35. (Pubitemid 41262914)
27. Qin SB, Zhou H-X (2007) meta-PPISP: a meta web server for protein-protein interaction site prediction. Bioinformatics, 23(24):3386-7.
28. Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, et al. (2005) Protein-protein docking benchmark 2.0: an update. Proteins, 60:214-216. (Pubitemid 40934889)
29. Neshich IAP, de Moraes FR, Salim JA, Mazoni I, Jardine JG, Neshich G (in press) Surface Hydrophobicity Index (SHI): Insights into the relationship between hydrophobic effect and oligomerization. Unpublished.
30. Barford D (2004) The role of cysteine residues as redox-sensitive regulatory switches. Curr Opin Struc Biol, 14(6):679-686.
31. Boatright KM, Salvesen GS (2003) Mechanisms of caspase activation. Curr Opin Cell Biol, 15:725-731. (Pubitemid 37492933)
32. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The Protein Data Bank. Nucleic Acids Res.,28(1):235-42. (Pubitemid 30047768)
33. Krissinel E, Henrick K (2007) Inference of macromolecular assemblies from crystalline state. J. Mol. Biol., 372:774-797. (Pubitemid 47321791)
34. Xu Q, Canutescu A,Wang G, Shapovalov M, Obradovic Z, Dunbrack Jr R (2008) Statistical Analysis of Interface Similarity in Crystals of Homologous Proteins.J.MolBiol, 381(2):487-507.
35. Bairoch A, Bougueleret L, Altairac S, Amendolia V, Auchincloss A, et al. (2009) The Universal Protein Resource (UniProt). Nucleic Acids Res., 37:D169-74.
36. Martin ACR (2005) Mapping PDB chains to UniProtKB entries. Bioinformatics, 21:4297-4301.
37. Scheneider M, Fu Xand Keating AE (2009) X-ray vs NMR structures as templates for computational protein design. Proteins, 77(1): 97-110.
38. BlueStar STING [(http://www.cbi.cnptia.embrapa.br/SMS/STINGm/help/ MegaHelp-JPD.html)]
39. Sridharan S, Nicholls A, Honig B (1992) A new vertex algorithm to calculate solvent accessible surface areas. Biophys. J., 61:A174.
40. Johnson DE (1998) Applied Multivariate Methods for Data Analysis Brooks/Cole Publishing Company.
41. Zar JH (1999) Biostatistical Analysis4th Edition Prentice Hall Inc.
42. Sing T, Sander O, Beerenwinkel N, Lengauer T (2005) ROCR: visualizing classifier performance in R. Bioinformatics, 21(20):3940-3941. (Pubitemid 41535515)
43. Fawcett T (2006) An introduction to ROC analysis. Pattern Recognition Letters, 27(8):861-874.
44. Da Silveira CH, Pires DEV, Minardi RC, Ribeiro C, Veloso CJM et al. (2009) Protein cutoff scanning: A comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins. Proteins, 74: 727-743.
45. Hwang H, Vreven T, Janin J, Weng Z (2010) Protein-protein docking benchmark version 4.0. Proteins. 78(15):3111-4.
46. Janin J (2010) "Protein-Protein docking tested in blind predictions: the CAPRI experiment". Mol BioSyst, 6:2351-2362.
47. Poupon A, Janin J (2010) "Analysis and prediction of protein quaternary structure". Methods Mol BIol 609:349-364
48. Vajda S, Kozakov D (2009) "Convergence and combination of methods in protein-protein docking". Curr Opin Struct Biol 19:164-170
49. Wass MN, David A, Sternberg MJ (2011) "Challenges for the prediction of macromolecular interactions". Curr Opin Struct Biol 21:382-390.
50. Tuncbag N, Gursoy A, Keskin O (2011) "Prediction of protein-protein interactions: unifying evolution and structure at protein interfaces". Phys Biol 8:035006
51. 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
52. 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.
53. Hamer R, Luo Q, Armitage JP, Reinert G, Deane CM (2010) "i-Patch: interprotein contact prediction using local network information", Proteins: Struct Funct Bioinform 78:2781-2797.
54. Ching-Tai Chen, Hung-Pin Peng, Jhih-Wei Jian, et al. (2012) "Protein-Protein Interaction Site Predictions with Three-Dimensional Probability Distributions of Interacting Atoms on Protein Surfaces". PlosOne, Vol 7, Issue 6, e37706.
55. Zhang QC, Petrey D, Norel R, Honig B (2010) "Protein Interface conservations across atructure space". Proc natl Acad Sci USA, 107:10896-10901.
56. Chandonia JM, Brenner SE (2006) The impact of structural genomics: expectations and outcomes. Science, Jan 20; 311(5759):347-51.
57. Bhattacharya A, Tejero R, Montelione GT (2007) Evaluating protein structures determined by structural genomics consortia. Proteins, Mar 1;66(4):778-95.
58. Terwilliger TC (2000) Structural genomics in North America. Nat Struct Biol. Nov 7, Suppl:935-9.
59. Tautz D, Domazet-Lošo T (2011) The evolutionary origin of orphan genes. Nat Rev Genet. Aug 31; 12(10):692-702.
60. Ekman D, Björklund AK, Frey-Skött J, Elofsson A (2005) Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions. J Mol Biol. Apr 22;348(1):231-43.
61. Murzin AG, Brenner SE, Hubbard T, Chothia C (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol. Apr 7;247(4):536-40.