UNIT 5.6 Comparative Protein Structure Modeling Using Modeller

  1. Narayanan Eswar,
  2. Ben Webb,
  3. Marc A. Marti-Renom,
  4. M.S. Madhusudhan,
  5. David Eramian,
  6. Min-yi Shen,
  7. Ursula Pieper,
  8. Andrej Sali

Published Online: 1 OCT 2006

DOI: 10.1002/0471250953.bi0506s15

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Eswar, N., Webb, B., Marti-Renom, M. A., Madhusudhan, M., Eramian, D., Shen, M.-y., Pieper, U. and Sali, A. 2006. Comparative Protein Structure Modeling Using Modeller. Current Protocols in Bioinformatics. 15:5.6:5.6.1–5.6.30.

Author Information

  1. University of California at San Francisco, San Francisco, California

Publication History

  1. Published Online: 1 OCT 2006
  2. Published Print: SEP 2006

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Functional characterization of a protein sequence is one of the most frequent problems in biology. This task is usually facilitated by accurate three-dimensional (3-D) structure of the studied protein. In the absence of an experimentally determined structure, comparative or homology modeling can sometimes provide a useful 3-D model for a protein that is related to at least one known protein structure. Comparative modeling predicts the 3-D 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 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.


  • Modeller;
  • protein structure;
  • comparative modeling;
  • structure prediction;
  • protein fold