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Pairwise and Multimeric Protein–Protein Docking Using the LZerD Program Suite

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Protein Structure Prediction

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1137))

Abstract

Physical interactions between proteins are involved in many important cell functions and are key for understanding the mechanisms of biological processes. Protein–protein docking programs provide a means to computationally construct three-dimensional (3D) models of a protein complex structure from its component protein units. A protein docking program takes two or more individual 3D protein structures, which are either experimentally solved or computationally modeled, and outputs a series of probable complex structures.

In this chapter we present the LZerD protein docking suite, which includes programs for pairwise docking, LZerD and PI-LZerD, and multiple protein docking, Multi-LZerD, developed by our group. PI-LZerD takes protein docking interface residues as additional input information. The methods use a combination of shape-based protein surface features as well as physics-based scoring terms to generate protein complex models. The programs are provided as stand-alone programs and can be downloaded from http://kiharalab.org/proteindocking.

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Acknowledgments

The authors thank Kristen Johnson for proofreading the manuscript. This work has been supported by grants from the National Institutes of Health (R01GM075004 and R01GM097528), National Science Foundation (EF0850009, DBI1262189, IOS1127027, IIS1319551), and National Research Foundation of Korea Grant funded by the Korean Government (NRF-2011-220-C00004). J.E.R. would like to thank the Fulbright Science and Technology program for supporting his first years of graduate studies.

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Authors and Affiliations

  1. Department of Computer Science, Purdue University, West Lafayette, IN, USA

    Juan Esquivel-Rodriguez & Daisuke Kihara

  2. Department of Mathematics, College of Science, Purdue University, West Lafayette, IN, USA

    Vianney Filos-Gonzalez

  3. La Jolla Institute for Allergy and Immunology, San Diego, CA, USA

    Bin Li

  4. Department of Biological Sciences, Purdue University, West Lafayette, IN, USA

    Daisuke Kihara

Authors
  1. Juan Esquivel-Rodriguez
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  2. Vianney Filos-Gonzalez
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  3. Bin Li
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  4. Daisuke Kihara
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Editors and Affiliations

  1. Purdue University Dept. Biological Science, West Lafayette, Indiana, USA

    Daisuke Kihara

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Esquivel-Rodriguez, J., Filos-Gonzalez, V., Li, B., Kihara, D. (2014). Pairwise and Multimeric Protein–Protein Docking Using the LZerD Program Suite. In: Kihara, D. (eds) Protein Structure Prediction. Methods in Molecular Biology, vol 1137. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0366-5_15

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  • DOI: https://doi.org/10.1007/978-1-4939-0366-5_15

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-0365-8

  • Online ISBN: 978-1-4939-0366-5

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