Benchmarking protein-protein interface predictions: Why you should care about protein size

Proteins: Structure, Function and Bioinformatics

Volumn 82, Issue 7, 2014, Pages 1444-1452

  Martin, Juliette ^a  

^a UNIVERSITÉ LYON 1   (France)

Author keywords

Assessment; Benchmark; Bias; Interface; Machine learning; Prediction; Protein; Protein protein interaction; Structure

Indexed keywords

PROTEIN; PROTEIN BINDING;

ARTICLE; BIOINFORMATICS; COMPUTER INTERFACE; COMPUTER PREDICTION; COMPUTER SIMULATION; CONTROLLED STUDY; MOLECULAR DOCKING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN SIZE; PROTEIN STRUCTURE; QUALITY CONTROL; BINDING SITE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; PARTICLE SIZE; PROTEIN DATABASE;

BINDING SITES; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATABASES, PROTEIN; MODELS, MOLECULAR; PARTICLE SIZE; PROTEIN BINDING; PROTEINS;

EID: 84902194040     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24512     Document Type: Article

References (23)

1. Jones S, Thornton JM. Principles of protein-protein interactions. Proc Natl Acad Sci USA 1996;93:13-20.
2. Chakrabarti P, Janin J. Dissecting protein-protein recognition sites. Proteins Struct Funct Bioinforma 2002;47:334-343.
3. Bickerton G, Higueruelo A, Blundell T. Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database. BMC Bioinformatics 2011;12:313.
4. Jones S, Thornton JM. Prediction of protein-protein interaction sites using patch analysis. J Mol Biol 1997;272:133-143.
5. Engelen S, Trojan LA, Sacquin-Mora S, Lavery R, Carbone A. Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling. PLoS Comput Biol 2009;5:e1000267.
6. Chen H, Zhou H-X. Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data. Proteins 2005;61:21-35.
7. Bradford JR, Westhead DR. Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics 2005;21:1487-1494.
8. 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;338:181-199.
9. Chung J-L, Wang W, Bourne PE. Exploiting sequence and structure homologs to identify protein-protein binding sites. Proteins Struct Funct Bioinforma 2005;62:630-640.
10. Fernández-Recio J. Prediction of protein binding sites and hot spots. Wiley Interdiscip Rev Comput Mol Sci 2011;1:680-698.
11. Zhou H-X, Shan Y. Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins Struct Funct Genet 2001;44:336-343.
12. Liang S, Zhang C, Liu S, Zhou Y. Protein binding site prediction using an empirical scoring function. Nucleic Acids Res 2006;34:3698-3707.
13. Qin S, Zhou H-X. meta-PPISP: a meta web server for protein-protein interaction site prediction. Bioinformatics 2007;23:3386-3387.
14. Jordan RA, EL-Manzalawy Y, Dobbs D, Honavar V. Predicting protein-protein interface residues using local surface structural similarity. BMC Bioinformatics 2012;13:41.
15. Segura J, Jones P, Fernandez-Fuentes N. Improving the prediction of protein binding sites by combining heterogeneous data and Voronoi Diagrams. BMC Bioinformatics 2011;12:352.
16. Hwang H, Vreven T, Janin J, Weng Z. Protein-protein docking benchmark version 4.0. Proteins Struct Funct Bioinforma 2010;78:3111-3114.
17. Hubbard SJ, Thornton JM. "NACCESS", computer programm. Department of Biochemistry and Molecular Biology, University College London.
18. Youden WJ. Index for rating diagnostic tests. Cancer 1950;3:32-35.
19. Robin X, Turck N, Hainard A, Tiberti N, Lisacek F, Sanchez J-C, Müller M. pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinformatics 2011;12:77.
20. DeLong ER, DeLong DM, Clarke-Pearson DL. Comparing the areas under two or more correlated receiver operating characteristic curves: a nonparametric approach. Biometrics 1988;44:837-845.
21. Martin J, Lavery R. Arbitrary protein-protein docking targets biologically relevant interfaces. BMC Biophys 2012;5:7.
22. Claus Bendtsen. pso: Particle Swarm Optimization; 2012.
23. Fernández-Recio J, Totrov M, Abagyan R. Identification of protein-protein interaction sites from docking energy landscapes. J Mol Biol 2004;335:843-865.