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Modeling of Multimolecular Complexes

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Structural Bioinformatics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2112))

Abstract

Macromolecular complexes play a key role in cellular function. Predicting the structure and dynamics of these complexes is one of the key challenges in structural biology. Docking applications have traditionally been used to predict pairwise interactions between proteins. However, few methods exist for modeling multi-protein assemblies. Here we present two methods, CombDock and DockStar, that can predict multi-protein assemblies starting from subunit structural models. CombDock can assemble subunits without any assumptions about the pairwise interactions between subunits, while DockStar relies on the interaction graph or, alternatively, a homology model or a cryo-electron microscopy (EM) density map of the entire complex. We demonstrate the two methods using RNA polymerase II with 12 subunits and TRiC/CCT chaperonin with 16 subunits.

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Acknowledgments

The work of D.S. is supported by the Israel Science Foundation (1466/18), Binational Science Foundation (2016070), and the Ministry of Science and Technology (80802). The work of H.J.W. was supported by the I-Core program of the Budgeting and Planning Committee and the Israel Science Foundation (Center No. 1775/12) and by Len Blavatnik and the Blavatnik Family Foundation.

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Authors and Affiliations

  1. School of Computer Science and Engineering and the Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel

    Dina Schneidman-Duhovny

  2. Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel

    Haim J. Wolfson

Authors
  1. Dina Schneidman-Duhovny
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  2. Haim J. Wolfson
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Corresponding author

Correspondence to Haim J. Wolfson .

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Editors and Affiliations

  1. Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary

    Zoltán Gáspári

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Schneidman-Duhovny, D., Wolfson, H.J. (2020). Modeling of Multimolecular Complexes. In: Gáspári, Z. (eds) Structural Bioinformatics. Methods in Molecular Biology, vol 2112. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0270-6_12

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  • DOI: https://doi.org/10.1007/978-1-0716-0270-6_12

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0269-0

  • Online ISBN: 978-1-0716-0270-6

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