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Bioinformatics Advance Access originally published online on September 6, 2007
Bioinformatics 2007 23(19):2558-2565; doi:10.1093/bioinformatics/btm377
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments

Narcis Fernandez-Fuentes , Brajesh K. Rai {dagger}, 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, Institute of Enzymology and Alfred Renyi Institute of Mathematics, Hungarian Academy of Sciences, H-1113 Budapest, Karolina ut 29, Hungary

*To whom correspondence should be addressed.


  Abstract

Motivation: Two major bottlenecks in advancing comparative protein structure modeling are the efficient combination of multiple template structures and the generation of a correct input target-template alignment.

Results: A novel method, Multiple Mapping Method with Multiple Templates (M4T) is introduced that implements an algorithm to automatically select and combine Multiple Template structures (MT) and an alignment optimization protocol (Multiple Mapping Method, MMM). The MT module of M4T selects and combines multiple template structures through an iterative clustering approach that takes into account the ‘unique’ contribution of each template, their sequence similarity among themselves and to the target sequence, and their experimental resolution. MMM is a sequence-to-structure alignment method that optimally combines alternatively aligned regions according to their fit in the structural environment of the template structure. The resulting M4T alignment is used as input to a comparative modeling module. The performance of M4T has been benchmarked on CASP6 comparative modeling target sequences and on a larger independent test set, and showed favorable performance to current state of the art methods.

Availability: A web server was established for the method at http://www.fiserlab.org/servers/M4T

Contact: afiser{at}aecom.yu.edu or andras{at}fiserlab.org

Associate Editor: Burkhard Rost

{dagger}Present address: Wyeth Research, CN8000, Princeton, New Jersey, 08543-8000, USA.

Received on March 8, 2007; revised on June 20, 2007; accepted on July 14, 2007

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