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Bioinformatics Advance Access published online on April 9, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp251
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

MICAlign: a sequence-to-structure alignment tool integrating multiple sources of information in conditional random fields

Xuefeng Xia {dagger}, Song Zhang {dagger}, Yu Su and Zhirong Sun *

Department of Biological Sciences and Biotechnology, MOE Key Laboratory of Bioinformatics, State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China

*To whom correspondence should be addressed. Zhirong Sun, E-mail: sunzhr{at}mail.tsinghua.edu.cn


  Abstract

Summary: Sequence-to-structure alignment in template-based protein structure modeling for remote homologues remains a difficult problem even following the correct recognition of folds. Here we present MICAlign, a sequence-to-structure alignment tool that incorporates multiple sources of information from local structural contexts of template, sequence profiles, predicted secondary structures, solvent accessibilities, potential-like terms (including residue-residue contacts and solvent exposures) and pre-aligned structures and sequences. These features, together with a position-specific gap scheme, were integrated into conditional random fields through which the optimal parameters were automatically learned. MICAlign showed improved alignment accuracy over several other state-of-the-art alignment tools based on comparisons by using independent datasets.

Availability: Freely available via http://www.bioinfo.tsinghua.edu.cn/~xiaxf/micalign for both web server and source code.

Contact: sunzhr{at}mail.tsinghua.edu.cn

Supplementary information: Supplementary data are available at Bioinformatics online

Associate Editor: Prof. Anna Tramontano

{dagger} The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

Received on January 15, 2009; revised on April 1, 2009; accepted on April 7, 2009

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