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Path-LZerD: Predicting Assembly Order of Multimeric Protein Complexes

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Protein-Protein Interaction Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2074))

Abstract

Many important functions in a cell are carried out by protein complexes with more than two subunits. Similar to the folding of a single protein, multimeric protein complexes in general follow an energetically favored assembly path. Knowing the assembly path not only provides critical information about the molecular mechanism of the assembly but also serves as a foundation for artificial design of protein complexes, as well as development of drugs that interfere with complex formation. There are experimental approaches for determining the assembly path of a complex; however, such methods are resource intensive. We have recently developed a computational method, Path-LZerD, which predicts the assembly path of a complex by simulating the docking process of the complex. Here, we explain how to use the Path-LZerD software with examples.

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Acknowledgments

We thank Tunde Aderinwale for testing this software. This work was partly supported by the National Institute of General Medical Sciences of the NIH (R01GM123055) and the National Science Foundation (DMS1614777).

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Authors and Affiliations

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

    Genki Terashi & Daisuke Kihara

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

    Charles Christoffer & Daisuke Kihara

Authors
  1. Genki Terashi
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  2. Charles Christoffer
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  3. Daisuke Kihara
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Corresponding author

Correspondence to Daisuke Kihara .

Editor information

Editors and Affiliations

  1. Gene Center, Ludwig-Maximilians-Universität München, München, Germany

    Stefan Canzar

  2. Gene Center, Ludwig-Maximilians-Universität München, München, Germany

    Francisca Rojas Ringeling

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Terashi, G., Christoffer, C., Kihara, D. (2020). Path-LZerD: Predicting Assembly Order of Multimeric Protein Complexes. In: Canzar, S., Ringeling, F. (eds) Protein-Protein Interaction Networks. Methods in Molecular Biology, vol 2074. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9873-9_8

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  • DOI: https://doi.org/10.1007/978-1-4939-9873-9_8

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9872-2

  • Online ISBN: 978-1-4939-9873-9

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