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Bioinformatics Advance Access published online on March 3, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti353
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received December 31, 2004
Revised February 22, 2005
Accepted February 23, 2005

Article

Multiple flexible structure alignment using partial order graphs

Yuzhen Ye 1* and Adam Godzik 1

1 The Burnham Institute, La Jolla, CA 92037, USA

* To whom correspondence should be addressed.
Yuzhen Ye, E-mail: yye{at}burnham.org


  Abstract

Motivation: Existing comparisons of protein structures are not able to describe structural divergence and flexibility in the structures being compared because they focus on identifying a common invariant core and ignore parts of the structures outside this core. Understanding the structural divergence and flexibility is critical for studying the evolution of functions and specificities of proteins.

Results: A new method of multiple protein structure alignment, POSA (Partial Order Structure Alignment), was developed using a partial order graph representation of multiple alignments. POSA has two unique features: (1) identifies and classifies regions that are conserved only in a subset of input structures, (2) allows internal rearrangements in protein structures. POSA outperforms other programs in cases in which structural flexibilities exist and provides new insights by visualizing the mosaic nature of multiple structural alignments. POSA is an ideal tool for studying the variation of protein structures within diverse structural families.

Availability: POSA is freely available for academic users on a Web server at http://fatcat.burnham.org/POSA.


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