Comparative Protein Structure Modeling Using MODELLER

Benjamin Webb1, Andrej Sali1

1 University of California at San Francisco, San Francisco, California
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 5.6
DOI:  10.1002/cpbi.3
Online Posting Date:  June, 2016
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Abstract

Comparative protein structure modeling predicts the three‐dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target‐template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and how to use the ModBase database of such models, and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described. © 2016 by John Wiley & Sons, Inc.

Keywords: comparative modeling; ModBase; MODELLER; protein fold; protein structure; structure prediction

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Modeling Lactate Dehydrogenase from Trichomonas Vaginalis (TvLDH) Based on a Single Template using Modeller
  • Support Protocol 1: Obtaining and Installing Modeller
  • Commentary
  • Figures
  • Tables
     
 
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Materials

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Literature Cited

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Internet Resources
  http://salilab.org/modeller/
  Webb, B., Madhusudhan, M.S., Shen, M‐Y., Dong, G.Q., Marti‐Renom, M.A., Eswar, N., Alber, F., Topf, M., Oliva, B., Fiser, A., Sanchez, R., Yerkovich, B., Badretdinov, A., Melo, F., Overington, J.P., Feyfant, E., and Sali, A. 2015. MODELLER, A Protein Structure Modeling Program, Release 9.15.
  http://salilab.org/modbase/
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  http://salilab.org/modloop/
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  http://salilab.org/allosmod/
  Weinkam, P., Pons, J., Webb, B., Pieper, U., Tjioe, E., and Sali, A. 2012. AllosMod, a web server to set up and run simulations based on modeled energy landscapes.
  http://salilab.org/foxs/
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