Prediction Of Protein-protein Binding Hot Spots: A Combination Of Classifiers Approach

In this work we approach the problem of predicting protein binding hot spot residues through a combination of classifiers. We consider a comprehensive set of structural and chemical properties reported in the literature for characterizing hot spot residues. Each component classifier considers a specific set of properties as feature set and their output are combined by the mean rule. The proposed combination of classifiers achieved a performance of 56.6%, measured by the F-Measure with corresponding Recall of 72.2% and Precision of 46.6%. This performance is higher than those reported by Darnel et al. [4] for the same data set, when compared through a t-test with a significance level of 5%. © 2008 Springer-Verlag Berlin Heidelberg.5167 LNBI165168Apweiler, R., Bairoch, A., Wu, C.H., UniProt: The Universal Protein Knowl-edgebase (2004) Nucl. Acid. Res, 32, pp. D115-D119Arkin, M.R., Wells, J.A., Small-Molecule Inhibitors of Protein-Protein Interactions: Progressing Towards the Dream (2004) Nature Reviews, Drug Discovery, 3, pp. 301-317Bussab, W.O., Morettin, P.A., (2002) Basic Statistics, , 5th edn. Editora Saraiva, São Paulo, Brazil , in PortugueseDarnell, S.J., Page, D., Mitchell, J.C., An Automated Decision-Tree Approach to Predicting Protein Interaction Hot Spots (2007) Proteins, 68, pp. 813-823Duin, R.P.W., Juszczak, P., Paclik, P., (2004) PRTools4, a Matlab Toolbox for Pattern Recognition, , Delft University of TechnologyHagerty, C.G., Munchnik, I., Kulikowski, C., Two Indices Can Approximate Four Hundred and Two Amino Acid Properties (1999) Proc. of 1999 IEEE Int. Simp. Intell. Control./Intell. Syst. and Semiotics, pp. 365-369. , Cambridge, MA, ppKortemme, T., Baker, D., A Simple Physical Model for Binding Energy Hot Spots in Protein-Protein Complexes (2002) Proc. Natl. Acad. Sci. USA, 99, pp. 14116-14121Liang, J., Edelsbrunner, H., Fu, P., Sudhakar, P.V., Analytical Shape Computation of Macromolecules: I. Molecular Area and Volume through Alpha Shape (1998) Proteins, 33, pp. 1-17Mancini, A.L., Higa, R.H., Oliveira, A., STING Contacts: A Web-Based application for Identification and Analysis of Amino Acid Contacts within Protein Structure and Across Protein Interfaces (2004) Bioinformatics, 20 (13), pp. 2145-2147Moreira, I.S., Fernandes, P.A., Ramos, M.J., Hot Spots - A Review of the Protein-Protein Interface Determinant Amino-Acid Residues (2007) Proteins, 68, pp. 803-812Pupko, R., Bell, R.E., Mayrose, I., Rate4Site: An Algorithmic Tool for the Identification of Functional Regions in Proteins by Surface Mapping of Evolutionary Determinants Within Their Homologues (2002) Bioinformatics, 18 (SUPL.1), pp. S71-S77Webb, A., (2002) Statistical Pattern Recognition, , Wiley, Chicheste