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Bioinformatics Advance Access originally published online on June 7, 2005
Bioinformatics 2005 21(15):3255-3263; doi:10.1093/bioinformatics/bti527
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

A new progressive-iterative algorithm for multiple structure alignment

Dmitry Lupyan 1, Alejandra Leo-Macias 2 and Angel R. Ortiz 2,*

1Department of Physiology and Biophysics, Mount Sinai School of Medicine One Gustave Levy Place, Box 1218, New York, 10029 NY USA
2Bioinformatics Unit, Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Universidad Autónoma de Madrid Cantoblanco, 28049 Madrid, Spain

*To whom correspondence should be addressed.

Motivation: Multiple structure alignments are becoming important tools in many aspects of structural bioinformatics. The current explosion in the number of available protein structures demands multiple structural alignment algorithms with an adequate balance of accuracy and speed, for large scale applications in structural genomics, protein structure prediction and protein classification.

Results: A new multiple structural alignment program, MAMMOTH-mult, is described. It is demonstrated that the alignments obtained with the new method are an improvement over previous manual or automatic alignments available in several widely used databases at all structural levels. Detailed analysis of the structural alignments for a few representative cases indicates that MAMMOTH-mult delivers biologically meaningful trees and conservation at the sequence and structural levels of functional motifs in the alignments. An important improvement over previous methods is the reduction in computational cost. Typical alignments take only a median time of 5 CPU seconds in a single R12000 processor. MAMMOTH-mult is particularly useful for large scale applications.

Availability: http://ub.cbm.uam.es/mammoth/mult

Contact: aro{at}cbm.uam.es

Received on April 28, 2005; revised on May 29, 2005; accepted on June 2, 2005

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