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Protein Structure Modeling with MODELLER

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Structural Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2199))

Abstract

Genome sequencing projects have resulted in a rapid increase in the number of known protein sequences. In contrast, only about one-hundredth of these sequences have been characterized at atomic resolution using experimental structure determination methods. Computational protein structure modeling techniques have the potential to bridge this sequence-structure gap. In the following chapter, we present an example that illustrates the use of MODELLER to construct a comparative model for a protein with unknown structure. Automation of a similar protocol has resulted in models of useful accuracy for domains in more than half of all known protein sequences.

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Acknowledgments

We are grateful to all members of our research group. This review is partially based on our previous reviews [60, 61]. We also acknowledge support from National Institutes of Health (U54 GM094625) as well as computing hardware support from Ron Conway, Mike Homer, Hewlett-Packard, NetApp, IBM, and Intel.

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Authors and Affiliations

  1. Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA

    Benjamin Webb & Andrej Sali

  2. Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA

    Benjamin Webb & Andrej Sali

  3. California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, CA, USA

    Benjamin Webb & Andrej Sali

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  1. Benjamin Webb
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  2. Andrej Sali
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Correspondence to Andrej Sali .

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Editors and Affiliations

  1. Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Hong Kong

    Yu Wai Chen

  2. BMI Biotechnology Appraisals & Investments Limited, Wan Chai, Hong Kong

    Chin-Pang Bennu Yiu

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Webb, B., Sali, A. (2021). Protein Structure Modeling with MODELLER. In: Chen, Y.W., Yiu, CP.B. (eds) Structural Genomics. Methods in Molecular Biology, vol 2199. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0892-0_14

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  • DOI: https://doi.org/10.1007/978-1-0716-0892-0_14

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0891-3

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