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Bioinformatics Advance Access originally published online on August 19, 2009
Bioinformatics 2009 25(20):2663-2669; doi:10.1093/bioinformatics/btp506
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

MISTRAL: a tool for energy-based multiple structural alignment of proteins

Cristian Micheletti 1,* and Henri Orland 2

1 SISSA, CNR-INFM Democritos and Italian Institute of Technology, Via Beirut 2-4, 34014 Trieste, Italy and 2 Institut de Physique Théorique, CEA, IPhT, F- 91191 Gif-sur-Yvette, France

* To whom correspondence should be addressed.


  Abstract

Motivation: The steady growth of the number of available protein structures has constantly motivated the development of new algorithms for detecting structural correspondences in proteins. Detecting structural equivalences in two or more proteins is computationally demanding as it typically entails the exploration of the combinatorial space of all possible amino acid pairings in the parent proteins. The search is often aided by the introduction of various constraints such as considering protein fragments, rather than single amino acids, and/or seeking only sequential correspondences in the given proteins. An additional challenge is represented by the difficulty of associating to a given alignment, a reliable a priori measure of its statistical significance.

Results: Here, we present and discuss MISTRAL (Multiple STRuctural ALignment), a novel strategy for multiple protein alignment based on the minimization of an energy function over the low-dimensional space of the relative rotations and translations of the molecules. The energy minimization avoids combinatorial searches and returns pairwise alignment scores for which a reliable a priori statistical significance can be given.

Availability: MISTRAL is freely available for academic users as a standalone program and as a web service at http://ipht.cea.fr/protein.php.

Contact: michelet{at}sissa.it

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Thomas Lengauer

Received on May 11, 2009; revised on July 20, 2009; accepted on August 13, 2009

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