ADMA '08 Proceedings of the 4th international conference on Advanced Data Mining and Applications
Model selection approaches for non-linear system identification: a review
International Journal of Systems Science
Research Article: Exploiting three kinds of interface propensities to identify protein binding sites
Computational Biology and Chemistry
Expert Systems with Applications: An International Journal
Learning a prediction model for protein-protein recognition
Proceedings of the 2nd International Conference on Interaction Sciences: Information Technology, Culture and Human
A Gaussian evolutionary method for predicting protein-protein interaction sites
EvoBIO'07 Proceedings of the 5th European conference on Evolutionary computation, machine learning and data mining in bioinformatics
Protein interface residues recognition using granular computing theory
RSKT'10 Proceedings of the 5th international conference on Rough set and knowledge technology
Identifying protein-protein interaction sites using granularity computing of quotient space theory
RSKT'10 Proceedings of the 5th international conference on Rough set and knowledge technology
Computing the protein binding sites
ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications
Prediction of protein-protein interface residues using sequence neighborhood and surface properties
ISNN'06 Proceedings of the Third international conference on Advances in Neural Networks - Volume Part III
Detection of Outlier Residues for Improving Interface Prediction in Protein Heterocomplexes
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
P-Binder: a system for the protein-protein binding sites identification
ISBRA'12 Proceedings of the 8th international conference on Bioinformatics Research and Applications
Detecting protein conformational changes in interactions via scaling known structures
RECOMB'13 Proceedings of the 17th international conference on Research in Computational Molecular Biology
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Identification of DNA-Binding and Protein-Binding Proteins Using Enhanced Graph Wavelet Features
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Predicting Protein-Ligand Binding Site Using Support Vector Machine with Protein Properties
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Motivation: Structural genomics projects are beginning to produce protein structures with unknown function, therefore, accurate, automated predictors of protein function are required if all these structures are to be properly annotated in reasonable time. Identifying the interface between two interacting proteins provides important clues to the function of a protein and can reduce the search space required by docking algorithms to predict the structures of complexes. Results: We have combined a support vector machine (SVM) approach with surface patch analysis to predict protein--protein binding sites. Using a leave-one-out cross-validation procedure, we were able to successfully predict the location of the binding site on 76% of our dataset made up of proteins with both transient and obligate interfaces. With heterogeneous cross-validation, where we trained the SVM on transient complexes to predict on obligate complexes (and vice versa), we still achieved comparable success rates to the leave-one-out cross-validation suggesting that sufficient properties are shared between transient and obligate interfaces. Availability: A web application based on the method can be found at http://www.bioinformatics.leeds.ac.uk/ppi_pred. The dataset of 180 proteins used in this study is also available via the same web site. Contact: westhead@bmb.leeds.ac.uk Supplementary information: http://www.bioinformatics.leeds.ac.uk/ppi-pred/supp-material