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Modeling of Protein Tertiary and Quaternary Structures Based on Evolutionary Information

  • Gabriel Studer
  • Gerardo Tauriello
  • Stefan Bienert
  • Andrew Mark Waterhouse
  • Martino Bertoni
  • Lorenza Bordoli
  • Torsten Schwede
  • Rosalba Lepore
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1851)

Abstract

Proteins are subject to evolutionary forces that shape their three-dimensional structure to meet specific functional demands. The knowledge of the structure of a protein is therefore instrumental to gain information about the molecular basis of its function. However, experimental structure determination is inherently time consuming and expensive, making it impossible to follow the explosion of sequence data deriving from genome-scale projects. As a consequence, computational structural modeling techniques have received much attention and established themselves as a valuable complement to experimental structural biology efforts. Among these, comparative modeling remains the method of choice to model the three-dimensional structure of a protein when homology to a protein of known structure can be detected.

The general strategy consists of using experimentally determined structures of proteins as templates for the generation of three-dimensional models of related family members (targets) of which the structure is unknown. This chapter provides a description of the individual steps needed to obtain a comparative model using SWISS-MODEL, one of the most widely used automated servers for protein structure homology modeling.

Key words

Homology modeling Oligomeric proteins Quaternary structure Protein structure prediction Model quality assessment Model quality estimates SWISS-MODEL 

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Gabriel Studer
    • 1
  • Gerardo Tauriello
    • 1
  • Stefan Bienert
    • 1
  • Andrew Mark Waterhouse
    • 1
  • Martino Bertoni
    • 1
  • Lorenza Bordoli
    • 1
  • Torsten Schwede
    • 1
  • Rosalba Lepore
    • 1
  1. 1.Biozentrum, University of Basel and SIB Swiss Institute of BioinformaticsBaselSwitzerland

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