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Methods Mol Biol. 2017;1654:39-54. doi: 10.1007/978-1-4939-7231-9_4.

Protein Structure Modeling with MODELLER.

Author information

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.
2
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. sali@salilab.org.

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.

KEYWORDS:

Comparative modeling; Fold assignment; Model assessment; Multiple templates; Sequence-structure alignment

PMID:
28986782
DOI:
10.1007/978-1-4939-7231-9_4
[Indexed for MEDLINE]

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