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Bioinformatics Advance Access originally published online on August 23, 2006
Bioinformatics 2006 22(21):2691-2692; 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

MMM: a sequence-to-structure alignment protocol

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

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.

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

Contact: andras{at}fiserlab.org

Received on June 2, 2006; revised on July 17, 2006; accepted on August 16, 2006

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