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Bioinformatics Vol. 19 no. 6 2003
Pages 735-741
© 2003 Oxford University Press

Protein structure comparison by probability-based matching of secondary structure elements

Edward S.C. Shih and Ming-Jing Hwang *

Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan

Received on October 10, 2002 ; revised on October 23, 2002 ; accepted on November 4, 2002

Motivation: Protein structure comparison (PSC) has been used widely in studies of structural and functional genomics. However, PSC is computationally expensive and as a result almost all of the PSC methods currently in use look only for the optimal alignment and ignore many alternative alignments that are statistically significant and that may provide insight into protein evolution or folding.

Results: We have developed a new PSC method with efficiency to detect potentially viable alternative alignments in all-against-all database comparisons. The efficiency of the new PSC method derives from the ability to directly home in on a limited number of viable and ranked alignment solutions based on intuitively derived SSE (secondary structure element)-matching probabilities.

Availability: The new PSC tool is accessible at our lab website http://gln.ibms.sinica.edu.tw/software.php

Contact: mjhwang{at}ibms.sinica.edu.tw

Supplementary Information: Supplementary tables and figures for this paper can be found at the same website.

* To whom correspondence should be addressed.


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Home page
 Nucleic Acids ResHome page
E. S. C. Shih, R.-c. R. Gan, and M.-J. Hwang
OPAAS: a web server for optimal, permuted, and other alternative alignments of protein structures.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W95 - W98.
[Abstract] [Full Text] [PDF]


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