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Modeling Protein Homo-Oligomer Structures with GalaxyHomomer Web Server

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Protein Structure Prediction

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2165))

Abstract

Cellular processes, such as metabolism, signal transduction, or immunity, often depend on the homo-oligomerization of proteins. Detailed structural knowledge of the homo-oligomer structure is therefore crucial for molecular-level understanding of protein functions and their regulation. In this chapter, we introduce the GalaxyHomomer server, which supports easy-to-use web interfaces for general users. It is freely accessible at http://galaxy.seoklab.org/homomer. GalaxyHomomer carries out template-based modeling, ab initio docking or both depending on the availability of proper oligomer templates. It also incorporates recently developed model refinement methods that can consistently improve model quality by performing symmetric loop modeling and overall structure refinement. Moreover, the server provides additional options that can be chosen by the user depending on the availability of information on the monomer structure, oligomeric state, and locations of unreliable/flexible loops or termini.

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Acknowledgments

The work was supported by National Research Foundation of Korea (NRF) grants funded by the Korean government (MSIT) [No. 2016M3C4A7952630].

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Author notes

  1. Minkyung Baek

    Present address: Department of Biochemistry, University of Washington, Seattle, WA, USA

  2. Lim Heo

    Present address: Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA

Authors and Affiliations

  1. Department of Chemistry, Seoul National University, Seoul, Republic of Korea

    Minkyung Baek, Taeyong Park, Lim Heo & Chaok Seok

Authors
  1. Minkyung Baek
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  2. Taeyong Park
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  3. Lim Heo
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  4. Chaok Seok
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Corresponding author

Correspondence to Chaok Seok .

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Editors and Affiliations

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

    Daisuke Kihara

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Baek, M., Park, T., Heo, L., Seok, C. (2020). Modeling Protein Homo-Oligomer Structures with GalaxyHomomer Web Server. In: Kihara, D. (eds) Protein Structure Prediction. Methods in Molecular Biology, vol 2165. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0708-4_7

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  • DOI: https://doi.org/10.1007/978-1-0716-0708-4_7

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0707-7

  • Online ISBN: 978-1-0716-0708-4

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