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

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

Author information

1
Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA.
2
Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.
3
Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA. dkihara@purdue.edu.
4
Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA. dkihara@purdue.edu.

Abstract

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 http://kiharalab.org/bindml/ and http://kiharalab.org/bindml/plus/ .

KEYWORDS:

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

PMID:
27914057
DOI:
10.1007/978-1-4939-6637-0_14
[Indexed for MEDLINE]

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