title: BindML/BindML+: Detecting Protein-Protein Interaction Interface Propensity from Amino Acid Substitution Patterns.
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/ .
authors.affiliation: Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA.
authors.forename: Qing
authors.initials: Q
authors.lastname: Wei
authors.affiliation: Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.
authors.forename: David
authors.initials: D
authors.lastname: La
authors.affiliation: Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA. dkihara@purdue.edu.|Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA. dkihara@purdue.edu.
authors.forename: Daisuke
authors.initials: D
authors.lastname: Kihara
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D054730:Protein Interaction Domains and Motifs; D011506:Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins
keywords: Bioinformatics; Interface residues; Protein binding site prediction; Protein docking; Protein interaction design; Protein interaction propensity; Protein-protein interaction