Skip Navigation


Bioinformatics Advance Access originally published online on June 7, 2005
Bioinformatics 2005 21(15):3255-3263; doi:10.1093/bioinformatics/bti527
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
21/15/3255    most recent
bti527v1
Right arrow Alert me when this article is cited
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 ISI Web of Science
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 arrow Search for citing articles in:
ISI Web of Science (29)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Lupyan, D.
Right arrow Articles by Ortiz, A. R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Lupyan, D.
Right arrow Articles by Ortiz, A. R.
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{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

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
Y. J. Qadri, B. K. Berdiev, Y. Song, H. L. Lippton, C. M. Fuller, and D. J. Benos
Psalmotoxin-1 Docking to Human Acid-sensing Ion Channel-1
J. Biol. Chem., June 26, 2009; 284(26): 17625 - 17633.
[Abstract] [Full Text] [PDF]


Home page
Mol. Pharmacol.Home page
J. Balzarini, I. Van Daele, A. Negri, N. Solaroli, A. Karlsson, S. Liekens, F. Gago, and S. Van Calenbergh
Human Mitochondrial Thymidine Kinase Is Selectively Inhibited by 3'-Thiourea Derivatives of {beta}-Thymidine: Identification of Residues Crucial for Both Inhibition and Catalytic Activity
Mol. Pharmacol., May 1, 2009; 75(5): 1127 - 1136.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
B. Pacheco, M. Maccarana, D. R. Goodlett, A. Malmstrom, and L. Malmstrom
Identification of the Active Site of DS-epimerase 1 and Requirement of N-Glycosylation for Enzyme Function
J. Biol. Chem., January 16, 2009; 284(3): 1741 - 1747.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
R. Mosca and T. R. Schneider
RAPIDO: a web server for the alignment of protein structures in the presence of conformational changes
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W42 - W46.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
A. Via, D. Peluso, P. F. Gherardini, E. de Rinaldis, T. Colombo, G. Ausiello, and M. Helmer-Citterich
3dLOGO: a web server for the identification, analysis and use of conserved protein substructures
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W416 - W419.
[Abstract] [Full Text] [PDF]


Home page
Brief BioinformHome page
P. Fariselli, I. Rossi, E. Capriotti, and R. Casadio
The WWWH of remote homolog detection: The state of the art
Brief Bioinform, March 1, 2007; 8(2): 78 - 87.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
H. Simader, M. Hothorn, C. Kohler, J. Basquin, G. Simos, and D. Suck
Structural basis of yeast aminoacyl-tRNA synthetase complex formation revealed by crystal structures of two binary sub-complexes
Nucleic Acids Res., September 1, 2006; 34(14): 3968 - 3979.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
Y. Chen and G. M. Crippen
An iterative refinement algorithm for consistency based multiple structural alignment methods
Bioinformatics, September 1, 2006; 22(17): 2087 - 2093.
[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.