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Comparative protein structure modeling using MODELLER.

Narayanan Eswar1, Ben Webb, Marc A Marti-Renom

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

Current Protocols in Protein Science
|April 23, 2008
PubMed
Summary
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This study details comparative protein modeling using MODELLER to predict 3-D structures when experimental data is unavailable. It covers fold assignment, alignment, model building, and evaluation, using lactate dehydrogenase as an example.

Area of Science:

  • Structural Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Accurate protein structures are 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.
  • To illustrate comparative modeling with a specific protein example.

Main Methods:

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

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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 a powerful tool for predicting protein 3-D structures.
  • The described methodology facilitates functional characterization in the absence of experimental data.
  • MODELS provides a comprehensive solution for homology modeling.