Journal Article

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

Xuefeng Xia, Song Zhang, Yu Su and Zhirong Sun

in Bioinformatics

Volume 25, issue 11, pages 1433-1434
Published in print June 2009 | ISSN: 1367-4803
Published online April 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp251
MICAlign: a sequence-to-structure alignment tool integrating multiple sources of information in conditional random fields

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Summary: Sequence-to-structure alignment in template-based protein structure modeling for remote homologs 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 at http://www.bioinfo.tsinghua.edu.cn/∼xiaxf/micalign for both web server and source code.

Contact: sunzhr@mail.tsinghua.edu.cn

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1296 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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