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

Methods Mol Biol. 2017;1529:279-289. doi: 10.1007/978-1-4939-6637-0_14.


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 .

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

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Binding Sites*
  • Computational Biology / methods*
  • Databases, Protein
  • Models, Molecular
  • Protein Binding
  • Protein Conformation
  • Protein Interaction Domains and Motifs*
  • Proteins* / chemistry
  • Proteins* / genetics
  • Proteins* / metabolism
  • Software*
  • User-Computer Interface


  • Proteins