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

Part of the Methods in Molecular Biology book series (MIMB,volume 1529)

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/.

Key words

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

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Acknowledgments

The authors thank Lyman Monroe for proofreading the manuscript. This work has been supported by grants from the National Institutes of Health (R01GM075004 and R01GM097528), National Science Foundation (IIS1319551, DBI1262189, IOS1127027), and National Research Foundation of Korea Grant funded by the Korean Government (NRF-2011-220-C00004).

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Correspondence to Daisuke Kihara .

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Wei, Q., La, D., Kihara, D. (2017). BindML/BindML+: Detecting Protein-Protein Interaction Interface Propensity from Amino Acid Substitution Patterns. In: Samish, I. (eds) Computational Protein Design. Methods in Molecular Biology, vol 1529. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6637-0_14

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  • DOI: https://doi.org/10.1007/978-1-4939-6637-0_14

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