Skip Navigation



Bioinformatics Advance Access published online on December 8, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti825
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow Supplementary Data
Right arrow All Versions of this Article:
22/4/504    most recent
bti825v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Eargle, J.
Right arrow Articles by Luthey-Schulten, Z.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Eargle, J.
Right arrow Articles by Luthey-Schulten, Z.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received July 29, 2005
Revised December 1, 2005
Accepted December 6, 2005

Applications note

Multiple Alignment of protein structures and sequences for VMD

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

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

* To whom correspondence should be addressed.
Zaida Luthey-Schulten, E-mail: multiseq{at}scs.uiuc.edu


  Abstract

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, 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.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 J. Biol. Chem.Home page
R. Carreno, D. Li, M. Sen, I. Nira, T. Yamakawa, Q. Ma, and G. B. Legge
A Mechanism for Antibody-mediated Outside-in Activation of LFA-1
J. Biol. Chem., April 18, 2008; 283(16): 10642 - 10648.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.