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Methods Mol Biol. 2017;1529:279-289.

BindML/BindML+: Detecting Protein-Protein Interaction Interface Propensity from Amino Acid Substitution Patterns.

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Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA.
Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.
Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA.
Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.


Prediction of protein-protein interaction sites in a protein structure provides important information for elucidating the mechanism of protein function and can also be useful in guiding a modeling or design procedures of protein complex structures. Since prediction methods essentially assess the propensity of amino acids that are likely to be part of a protein docking interface, they can help in designing protein-protein interactions. Here, we introduce BindML and BindML+ protein-protein interaction sites prediction methods. BindML predicts protein-protein interaction sites by identifying mutation patterns found in known protein-protein complexes using phylogenetic substitution models. BindML+ is an extension of BindML for distinguishing permanent and transient types of protein-protein interaction sites. We developed an interactive web-server that provides a convenient interface to assist in structural visualization of protein-protein interactions site predictions. The input data for the web-server are a tertiary structure of interest. BindML and BindML+ are available at and .


Bioinformatics; Interface residues; Protein binding site prediction; Protein docking; Protein interaction design; Protein interaction propensity; Protein-protein interaction

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