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Bioinformatics Advance Access originally published online on December 8, 2005
Bioinformatics 2006 22(4):504-506; doi:10.1093/bioinformatics/bti825
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Multiple Alignment of protein structures and sequences for VMD

John Eargle 1, Dan Wright 2,3 and Zaida Luthey-Schulten 1,3,*

1Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign 607 South Mathews Avenue, Urbana, IL 61801, USA
2Graduate School of Library and Information Sciences, University of Illinois at Urbana-Champaign 501 Daniel Street, Champaign, IL 61820, USA
3Department of Chemistry, University of Illinois at Urbana-Champaign 505 South Mathews Avenue, Urbana, IL 61801, USA

*To whom correspondence should be addressed.

Multiple Alignment is a new interface for performing and analyzing multiple protein structure alignments. It enables viewing levels of sequence and structure similarity on the aligned structures and performing a variety of evolutionary and bioinformatic tasks, including the construction of structure-based phylogenetic trees and minimal basis sets of structures that best represent the topology of the phylogenetic tree. It is implemented as a plugin for VMD (Visual Molecular Dynamics), which is distributed by the NIH Resource for Macromolecular Modeling and Bioinformatics at the University of Illinois.

Availability: Both binary and source code downloads for VMD 1.83, which includes Multiple Alignment, are available from http://www.ks.uiuc.edu/Research/vmd/. The Multidimensional QR factorization algorithm is available at http://www.scs.uiuc.edu/~schulten/software.html

Contact: multiseq{at}scs.uiuc.edu

Received on July 29, 2005; revised on December 1, 2005; accepted on December 6, 2005

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