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Prediction of protein-protein interactions based on surface patch comparison.

Oliviero Carugo·Giacomo Franzot
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Abstract

A method to predict if two proteins interact, based on their three-dimensional structures, is presented. It consists of five steps: (i) the surface of each protein, represented by the solvent accessible atoms, is divided into small patches; (ii) the shape of each patch is described by the atom distributions along its principal axes; (iii) the shape complementarity between two patches is estimated by comparing, through contingency table analysis, their atom distributions along their principal axes; (iv) given protein A, with nA surface patches, and protein B, with nB surface patches, nA x nB shape complementarity values are obtained; and (v) the distribution of the latter allows one to discriminate pairs of interacting and of noninteracting proteins. Only a few seconds are necessary to predict if two proteins interact, with accuracy close to 80%, sensitivity over 70% and specificity close to 50%.

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Computational BiologyDatabases, FactualImaging, Three-DimensionalModels, MolecularMolecular ConformationProtein BindingProteinsSensitivity and SpecificitySurface PropertiesComparative StudyJournal Article

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Oliviero Carugo, Giacomo Franzot. 2004. Prediction of protein-protein interactions based on surface patch comparison.. https://doi.org/10.1002/pmic.200300692

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