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Bioinformatics Advance Access originally published online on May 5, 2009
Bioinformatics 2009 25(13):1625-1631; doi:10.1093/bioinformatics/btp296
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Flexible structural protein alignment by a sequence of local transformations

Jairo Rocha 1,*, Joan Segura 1, Richard C. Wilson 2 and Swagata Dasgupta 3

1Department of Mathematics and Computer Science, University of the Balearic Islands, Palma, E07122, Spain, 2Department of Computer Science, University of York, YO1 0 5DD, UK and 3Department of Chemistry, Indian Institute of Technology, Kharagpur 721 302, India

*To whom correspondence should be addressed.


  Abstract

Motivation: Throughout evolution, homologous proteins have common regions that stay semi-rigid relative to each other and other parts that vary in a more noticeable way. In order to compare the increasing number of structures in the PDB, flexible geometrical alignments are needed, that are reliable and easy to use.

Results: We present a protein structure alignment method whose main feature is the ability to consider different rigid transformations at different sites, allowing for deformations beyond a global rigid transformation. The performance of the method is comparable with that of the best ones from 10 aligners tested, regarding both the quality of the alignments with respect to hand curated ones, and the classification ability. An analysis of some structure pairs from the literature that need to be matched in a flexible fashion are shown. The use of a series of local transformations can be exported to other classifiers, and a future golden protein similarity measure could benefit from it.

Availability: A public server for the program is available at http://dmi.uib.es/ProtDeform/.

Contact: jairo{at}uib.es

Supplementary information: All data used, results and examples are available at http://dmi.uib.es/people/jairo/bio/ProtDeform.Supplementary data are available at Bioinformatics online.

Associate Editor: Anna Tramontano

Received on November 9, 2008; revised on April 23, 2009; accepted on April 29, 2009

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