Skip Navigation

This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
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 (15)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Jewett, A. I.
Right arrow Articles by Ferrin, T. E.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Jewett, A. I.
Right arrow Articles by Ferrin, T. E.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics Vol. 19 no. 5 2003
Pages 625-634
© 2003 Oxford University Press

MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance

Andrew I. Jewett , Conrad C. Huang and Thomas E. Ferrin *

Computer Graphics Laboratory, Department of Pharmaceutical Chemistry, University of California at San Fransisco, San Fransisco, CA 94143-0446 USA

Received on November 1, 2000 ; revised on January 30, 2001 and October 17, 2002 ; accepted on November 7, 2002

Motivation: Existing algorithms for automated protein structure alignment generate contradictory results and are difficult to interpret. An algorithm which can provide a context for interpreting the alignment and uses a simple method to characterize protein structure similarity is needed.

Results: We describe a heuristic for limiting the search space for structure alignment comparisons between two proteins, and an algorithm for finding minimal root-mean-squared-distance (RMSD) alignments as a function of the number of matching residue pairs within this limited search space. Our alignment algorithm uses coordinates of alpha-carbon atoms to represent each amino acid residue and requires a total computation time of O(m3 n2), where m and n denote the lengths of the protein sequences. This makes our method fast enough for comparisons of moderate-size proteins (fewer than ~800 residues) on current workstation-class computers and therefore addresses the need for a systematic analysis of multiple plausible shape similarities between two proteins using a widely accepted comparison metric.

Availability: See http://www.cgl.ucsf.edu/Research/minrms

Contact: tef{at}cgl.ucsf.edu

* To whom correspondence should be addressed.


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
 Biophys. JHome page
K. L. Damm and H. A. Carlson
Gaussian-Weighted RMSD Superposition of Proteins: A Structural Comparison for Flexible Proteins and Predicted Protein Structures
Biophys. J., June 15, 2006; 90(12): 4558 - 4573.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
H.-C. HUANG, U. NAGASWAMY, and G. E. FOX
The application of cluster analysis in the intercomparison of loop structures in RNA
RNA, April 1, 2005; 11(4): 412 - 423.
[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.