Journal Article

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

Cristian Micheletti and Henri Orland

in Bioinformatics

Volume 25, issue 20, pages 2663-2669
Published in print October 2009 | ISSN: 1367-4803
Published online August 2009 | e-ISSN: 1460-2059 | DOI:
MISTRAL: a tool for energy-based multiple structural alignment of proteins

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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


Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  6206 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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