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Bioinformatics Vol. 18 no. 4 2002
Pages 637-640
© 2002 Oxford University Press

Applications Note

Advanced pairwise structure alignments of proteins and analysis of conformational changes

Maria Elena Ochagavia 1,2, Jean Richelle 2 and Shoshana J. Wodak 2,*

1 Center for Genetic Engineering and Biotechnology, Ave. 31 between Avenues 158 and 190, Cubanacán, City of Havana, 10600 Cuba
2 Service de Conformation de Macromolécules Biologiques et de Bioinformatique CP 160/16, P2, UniversitéLibre de Bruxelles, Ave. F. Roosevelt, 1050 Bruxelles, Belgium

Received on July 18, 2001 ; revised on October 30, 2001 ; accepted on November 14, 2001

Motivation: Comparing the 3D structures of two proteins or analyzing the structural changes undergone by a protein upon ligand binding or when it crystallizes under different conditions, can be both tricky and tedious, especially when the two proteins are distantly related, or when the structural changes are complex. Readily accessible tools for performing these tasks automatically and reliably should therefore be welcome.

Results: We describe a web interface to several automatic procedures for performing pairwise structure superposition in a flexible manner, for detailed analyses of conformational changes and for displaying the results in a pictorial fashion.

Availability: This interface can be accessed at the Brussels and Cuba Web sites, respectively: http://www.ucmb.ulb.ac.be/SCMBB/Tools.htmland http://bio.cigb.edu.cu.

Contact: shosh{at}ucmb.ulb.ac.be

* To whom correspondence should be addressed.


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