PredHS: A web server for predicting protein-protein interaction hot spots by using structural neighborhood properties

Nucleic Acids Research

Volumn 42, Issue W1, 2014, Pages

  Deng, Lei ^a,b   Zhang, Qiangfeng Cliff ^c   Chen, Zhigang ^a   Meng, Yang ^a   Guan, Jihong ^b   Zhou, Shuigeng ^d  

^a CENTRAL SOUTH UNIVERSITY   (China)

^b TONGJI UNIVERSITY   (China)

^c Och Spine at New York Presbyterian Hospitals   (United States)

^d FUDAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; AREA UNDER THE CURVE; ARTICLE; AUTOMATION; COMPUTER INTERFACE; COMPUTER PREDICTION; COMPUTER PROGRAM; DATA PROCESSING; DATA RECALL; DATA SPECIFICITY; INFORMATION RETRIEVAL; INTERMETHOD COMPARISON; MATHEMATICAL COMPUTING; MEASUREMENT ACCURACY; ONLINE SYSTEM; PERFORMANCE MEASUREMENT SYSTEM; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; WEB BROWSER;

ALGORITHMS; INTERNET; MODELS, MOLECULAR; MULTIPROTEIN COMPLEXES; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPPING; SOFTWARE;

EID: 84904803244     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku437     Document Type: Article

References (38)

1. Clackson,T. and Wells,J.A. (1995) A hot spot of binding energy in a hormone-receptor interface. Science (New York, N.Y.), 267, 383-386.
2. Wells,J.A. and McClendon,C.L. (2007) Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature, 450, 1001-1009.
3. Thorn,K.S. and Bogan,A.A. (2001) ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions. Bioinformatics, 17, 284-285.
4. Fischer,T.B., Arunachalam,K.V., Bailey,D., Mangual,V., Bakhru,S., Russo,R., Huang,D., Paczkowski,M., Lalchandani,V., Ramachandra,C. et al. (2003) The binding interface database (BID): a compilation of amino acid hot spots in protein interfaces. Bioinformatics, 19, 1453-1454.
5. Massova,I. and Kollman,P.A. (1999) Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies. J. Am. Chem. Soc., 121, 8133-8143.
6. Grosdidier,S. and Fernandez-Recio,J. (2008) Identification of hot-spot residues in protein-protein interactions by computational docking. BMC Bioinformatics, 9, 447.
7. Brenke,R., Kozakov,D., Chuang,G.Y., Beglov,D., Hall,D., Landon,M.R., Mattos,C. and Vajda,S. (2009) Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques. Bioinformatics, 25, 621-627.
8. Huo,S., Massova,I. and Kollman,P.A. (2002) Computational alanine scanning of the 1:1 human growth hormone-receptor complex. J. Comput. Chem., 23, 15-27.
9. Guerois,R., Nielsen,J.E. and Serrano,L. (2002) Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J. Mol. Biol., 320, 369-387.
10. Kortemme,T. and Baker,D. (2002) A simple physical model for binding energy hot spots in protein-protein complexes. Proc. Natl. Acad. Sci. U.S.A., 99, 14116-14121.
11. Ofran,Y. and Rost,B. (2007) Protein-protein interaction hot spots carved into sequences. PLoS Comput. Biol., 3, e119.
12. Darnell,S.J., Page,D. and Mitchell,J.C. (2007) An automated decision-tree approach to predicting protein interaction hot spots. Proteins, 68, 813-823.
13. Cho,K.I., Kim,D. and Lee,D. (2009) A feature-based approach to modeling protein-protein interaction hot spots. Nucleic Acids Res., 37, 2672-2687.
14. Xia,J.F., Zhao,X.M., Song,J. and Huang,D.S. (2010) APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility. BMC Bioinformatics, 11, 174.
15. Zhu,X. and Mitchell,J.C. (2011) KFC2: a knowledge-based hot spot prediction method based on interface solvation, atomic density, and plasticity features. Proteins, 79, 2671-2683.
16. Assi,S.A., Tanaka,T., Rabbitts,T.H. and Fernandez-Fuentes,N. (2010) PCRPi: presaging critical residues in protein interfaces, a new computational tool to chart hot spots in protein interfaces. Nucleic Acids Res., 38, e86.
17. Segura,J. and Fernandez-Fuentes,N. (2011) PCRPi-DB: a database of computationally annotated hot spots in protein interfaces. Nucleic Acids Res., 39, D755-760.
18. Tuncbag,N., Gursoy,A. and Keskin,O. (2009) Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy. Bioinformatics, 25, 1513-1520.
19. Wang,L., Liu,Z.P., Zhang,X.S. and Chen,L. (2012) Prediction of hot spots in protein interfaces using a random forest model with hybrid features. Protein Eng. Des. Sel., 25, 119-126.
20. Cukuroglu,E., Gursoy,A. and Keskin,O. (2012) HotRegion: a database of predicted hot spot clusters. Nucleic Acids Res., 40, D829-D833.
21. Guney,E., Tuncbag,N., Keskin,O. and Gursoy,A. (2008) HotSprint: database of computational hot spots in protein interfaces. Nucleic Acids Res., 36, D662-D666.
22. Deng,L., Guan,J., Wei,X., Yi,Y., Zhang,Q.C. and Zhou,S. (2013) Boosting prediction performance of protein-protein interaction hot spots by using structural neighborhood properties. J. Comput. Biol., 20, 878-891.
23. Chan,C.H., Liang,H.K., Hsiao,N.W., Ko,M.T., Lyu,P.C. and Hwang,J.K. (2004) Relationship between local structural entropy and protein thermostability. Proteins, 57, 684-691.
24. Liang,S. and Grishin,N.V. (2004) Effective scoring function for protein sequence design. Proteins, 54, 271-281.
25. Krishnamoorthy,B. and Tropsha,A. (2003) Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations. Bioinformatics, 19, 1540-1548.
26. Levy,E.D. (2007) PiQSi: protein quaternary structure investigation. Structure (London, England:1993), 15, 1364-1367.
27. Okabe,A., Boots,B. and Sugihara,K. (1992) Spatial Tessellations: Concepts and Applications of Voronoi Diagrams. John Wiley & Sons, Inc, Hoboken, New Jersey, United States, 65-115.
28. Barber,C.B., Dobkin,D.P. and Huhdanpaa,H. (1996) The quickhull algorithm for convex hulls. ACM Trans. Math. Softw., 22, 469-483.
29. Segura,J., Jones,P.F. and Fernandez-Fuentes,N. (2011) Improving the prediction of protein binding sites by combining heterogeneous data and Voronoi diagrams. BMC Bioinformatics, 12, 352.
30. Liaw,A. and Wiener,M. (2002) Classification and regression by randomForest.R News, 2, 18-22.
31. Chang,C.-C. and Lin,C.-J. (2011) LIBSVM: a library for support vector machines. ACM Trans. Intell. Syst. Technol., 2, 1-27.
32. Hartshorn,M.J. (2002) AstexViewer: a visualisation aid for structure-based drug design. J. Comput. Aided Mol. Des., 16, 871-881.
33. Deng,L., Guan,J., Dong,Q. and Zhou,S. (2009) Prediction of protein-protein interaction sites using an ensemble method. BMC Bioinformatics, 10, 426.
34. Kawashima,S. and Kanehisa,M. (2000) AAindex: amino acid index database. Nucleic Acids Res., 28, 374.
35. Kabsch,W. and Sander,C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
36. Keskin,O., Bahar,I., Badretdinov,A.Y., Ptitsyn,O.B. and Jernigan,R.L. (1998) Empirical solvent-mediated potentials hold for both intra-molecular and inter-molecular inter-residue interactions. Protein Sci., 7, 2578-2586.
37. Hu,L., Cui,W., He,Z., Shi,X., Feng,K., Ma,B. and Cai,Y.D. (2012) Cooperativity among short amyloid stretches in long amyloidogenic sequences. PloS One, 7, e39369.
38. Tuncbag,N., Keskin,O. and Gursoy,A. (2010) HotPoint: hot spot prediction server for protein interfaces. Nucleic Acids Res., 38, W402-W406.