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Functional Genomics pp 39–54Cite as

Protein Structure Modeling with MODELLER

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1654))

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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Acknowledgements

We are grateful to all members of our research group. 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, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, CA, 94143, 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. Chair of Biochemistry and Molecular Medicine, Division of Functional Genomics, Faculty of Health, School of Medicine, Center for Biochemical Research and Education ZBAF, Witten/Herdecke University, Witten, Germany

    Michael Kaufmann

  2. Chair of Biochemistry and Molecular Medicine, Division of Functional Genomics, Faculty of Health, School of Medicine, Center for Biochemical Research and Education ZBAF, Witten/Herdecke University, Witten, Germany

    Claudia Klinger

  3. Chair of Biochemistry and Molecular Medicine, Division of Functional Genomics, Faculty of Health, School of Medicine, Center for Biochemical Research and Education ZBAF, Witten/Herdecke University, Witten, Germany

    Andreas Savelsbergh

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Webb, B., Sali, A. (2017). Protein Structure Modeling with MODELLER. In: Kaufmann, M., Klinger, C., Savelsbergh, A. (eds) Functional Genomics. Methods in Molecular Biology, vol 1654. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7231-9_4

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  • DOI: https://doi.org/10.1007/978-1-4939-7231-9_4

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