Protein Structure Prediction pp 1-15

Part of the Methods in Molecular Biology book series (MIMB, volume 1137)

| Cite as

Protein Structure Modeling with MODELLER

  • Benjamin Webb
  • Andrej Sali
Protocol

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 this 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 Sequence–structure alignment Model assessment Multiple templates 

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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Benjamin Webb
    • 1
    • 2
  • Andrej Sali
    • 1
    • 2
  1. 1.Department of Bioengineering and Therapeutic SciencesUniversity of CaliforniaSan FranciscoUSA
  2. 2.Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences (QB3)University of California San FranciscoSan FranciscoUSA

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