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Biological processes are commonly controlled by precise protein-protein interactions. These connections rely on specific amino acids at the binding interfaces. Here we predict the binding residues of such interprotein complexes. We have developed a suite of methods, i-Patch, which predict the interprotein contact sites by considering the two proteins as a network, with residues as nodes and contacts as edges. i-Patch starts with two proteins, A and B, which are assumed to interact, but for which the structure of the complex is not available. However, we assume that for each protein, we have a reference structure and a multiple sequence alignment of homologues. i-Patch then uses the propensities of patches of residues to interact, to predict interprotein contact sites. i-Patch outperforms several other tested algorithms for prediction of interprotein contact sites. It gives 59% precision with 20% recall on a blind test set of 31 protein pairs. Combining the i-Patch scores with an existing correlated mutation algorithm, McBASC, using a logistic model gave little improvement. Results from a case study, on bacterial chemotaxis protein complexes, demonstrate that our predictions can identify contact residues, as well as suggesting unknown interfaces in multiprotein complexes.

Original publication

DOI

10.1002/prot.22792

Type

Journal article

Journal

Proteins

Publication Date

10/2010

Volume

78

Pages

2781 - 2797

Keywords

Algorithms, Amino Acid Sequence, Bacterial Proteins, Binding Sites, Computational Biology, Membrane Proteins, Methyl-Accepting Chemotaxis Proteins, Models, Molecular, Molecular Sequence Data, Protein Binding, Protein Interaction Mapping, Protein Structure, Tertiary, Proteins, Reproducibility of Results, Sequence Homology, Amino Acid