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Related Experiment Videos

Comparative protein structure modeling using Modeller.

Narayanan Eswar1, Ben Webb1, Marc A Marti-Renom1

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

Current Protocols in Bioinformatics
|April 23, 2008
PubMed
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Comparative modeling predicts protein 3-D structures using known related proteins. This guide details the MODELLER software for homology modeling, covering fold assignment, alignment, building, and evaluation, with a lactate dehydrogenase example.

Area of Science:

  • Structural biology
  • Computational biology
  • Bioinformatics

Background:

  • Determining protein 3-D structure is crucial for functional characterization.
  • Experimental structure determination is not always feasible.
  • Homology modeling offers a viable alternative for predicting protein structures.

Purpose of the Study:

  • To describe the process of comparative protein modeling.
  • To provide a guide for using the MODELLER software for homology modeling.
  • To illustrate the application of comparative modeling using an example.

Main Methods:

  • Comparative modeling based on sequence alignment to known structures (templates).
  • Utilizing the MODELLER software package.
  • Detailed explanation of fold assignment, target-template alignment, model building, and evaluation steps.

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Main Results:

  • Successful application of MODELLER for comparative modeling.
  • Demonstration of modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH).
  • Discussion of common errors and applications in comparative modeling.

Conclusions:

  • Comparative modeling with MODELLER is an effective method for predicting protein 3-D structures.
  • The described methodology facilitates functional characterization of proteins lacking experimental structures.
  • MODFFELLER provides a comprehensive tool for homology modeling in structural biology.