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Bioinformatics Advance Access published online on August 23, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl449
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received June 2, 2006
Revised July 17, 2006
Accepted August 16, 2006

Applications note

MMM: a sequence-to-structure alignment protocol

Brajesh K. Rai 1, Carlos J. Madrid-Aliste 1, J. Eduardo Fajardo 1, and András Fiser 1 *

1 Department of Biochemistry and Seaver Center for Bioinformatics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 USA

* To whom correspondence should be addressed.
András Fiser, E-mail: andras{at}fiserlab.org


  Abstract

Motivation: Accurate alignment of a target sequence to a template structure continues to be a bottleneck in producing good quality comparative protein structure models.

Results: Multiple Mapping Method (MMM) is a comparative protein structure modeling server with an emphasis on a novel alignment optimization protocol. MMM takes inputs from five profile-to-profile based alignment methods. The alternatively aligned regions from the input alignment set are combined according to their fit in the structural environment of the template structure. The resulting, optimally spliced MMM alignment is used as input to an automated comparative modeling module to produce a full atom model.

Availability: The MMM server is freely accessible at: http://www.fiserlab.org/servers/mmm.

Associate Editor: Martin Bishop
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