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Bioinformatics Advance Access originally published online on June 15, 2009
Bioinformatics 2009 25(15):1963-1965; doi:10.1093/bioinformatics/btp335
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

InterMap3D: predicting and visualizing co-evolving protein residues

Rodrigo Gouveia-Oliveira {dagger}, Francisco S. Roque {dagger}, Rasmus Wernersson , Thomas Sicheritz-Ponten , Peter W. Sackett , Anne Mølgaard and Anders G. Pedersen *

Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark

* To whom correspondence should be addressed.


  Abstract

Summary: InterMap3D predicts co-evolving protein residues and plots them on the 3D protein structure. Starting with a single protein sequence, InterMap3D automatically finds a set of homologous sequences, generates an alignment and fetches the most similar 3D structure from the Protein Data Bank (PDB). It can also accept a user-generated alignment. Based on the alignment, co-evolving residues are then predicted using three different methods: Row and Column Weighing of Mutual Information, Mutual Information/Entropy and Dependency. Finally, InterMap3D generates high-quality images of the protein with the predicted co-evolving residues highlighted.

Availability: http://www.cbs.dtu.dk/services/InterMap3D/

Contact: gorm{at}cbs.dtu.dk

{dagger} These authors contributed equally.

Associate Editor: Thomas Lengauer

Received on January 31, 2009; revised on April 29, 2009; accepted on May 26, 2009

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