i-Patch: interprotein contact prediction using local network information

Proteins
Rebecca HamerCharlotte M Deane

Abstract

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 u...Continue Reading

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Citations

Sep 6, 2013·Protein Engineering, Design & Selection : PEDS·Konrad KrawczykCharlotte M Deane
Dec 19, 2012·BMC Research Notes·Mireille GomesCharlotte M Deane
Mar 23, 2013·PloS One·Qiang LuoCharlotte M Deane
May 24, 2014·Archives of Biochemistry and Biophysics·Jessica Andreani, Raphael Guerois
Dec 4, 2015·Journal of Chemical Information and Modeling·Bernhard Knapp, Charlotte M Deane
May 15, 2015·Briefings in Bioinformatics·Reyhaneh EsmaielbeikiCharlotte M Deane
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Feb 27, 2020·Current Topics in Medicinal Chemistry·Olivia SlaterMaria Kontoyianni
Nov 12, 2020·PLoS Computational Biology·Duncan K Ralph, Frederick A Matsen
May 18, 2021·Frontiers in Molecular Biosciences·Zahra Sadat HashemiSaeed Khalili

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