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Bioinformatics Advance Access published online on April 21, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti438
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received February 23, 2005
Revised April 2, 2005
Accepted April 6, 2005

Applications note

MolIDE (Molecular Integrated Development Environment): a homology modeling framework you can click with

Adrian A. Canutescu 1* and Roland L. Dunbrack Jr.1

1 Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia PA 19111, USA

* To whom correspondence should be addressed.
Adrian A. Canutescu, E-mail: Adrian.Canutescu{at}fccc.edu


  Abstract

Summary: MolIDE is an integrated application designed to provide homology modeling tools and protocols under a uniform, user-friendly graphical interface. Its main purpose is to combine the most frequent modeling steps in a semi-automatic, interactive way, guiding the user from the target protein sequence to the final three-dimensional protein structure. The typical basic homology modeling process is composed of building sequence profiles of the target sequence family, secondary structure prediction, sequence alignment with PDB structures, assisted alignment editing, side-chain prediction and loop building. All of these steps are available through a graphical user interface. MolIDE's user-friendly and stream-lined interactive modeling protocol allows the user to focus on the important modeling questions, hiding from the user the raw data generation and conversion steps. MolIDE was designed from ground up as an open-source, cross-platform, extensible framework. This allows developers to integrate additional third-party programs to MolIDE.

Availability: http://dunbrack.fccc.edu/molide/molide.php.


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