Nucleic Acids Research, 2003, Vol. 31, No. 1 505-510
© 2003 Oxford University Press
The Structure Superposition Database
1 Department of Biopharmaceutical Sciences, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA 2 Department of Pharmaceutical Chemistry, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
*To whom correspondence should be addressed. Tel: +1 415 476 3784; Fax: +1 415 476 0668; Email: babbitt{at}cgl.ucsf.edu
ABSTRACT
The need for new tools for investigating biological systems on a large scale is becoming acute, particularly with respect to computationally intensive analyses such as comparisons of many three-dimensional protein structures. Structure superposition is a valuable approach for understanding evolutionary relationships and for the prediction of function. But while available tools are adequate for generating and viewing superpositions of single pairs of protein structures, these tools are generally too cumbersome and time-consuming for examining multiple superpositions. To address this need, we have created the Structure Superposition Database (SSD) for accessing, viewing and understanding large sets of structure superposition data. The initial implementation of the SSD contains the results of pairwise, all-by-all superpositions of a representative set of 115 (ß/
)8 barrel structures (TIM barrels). Future plans call for extending the database to include representative structure superpositions for many additional folds. The SSD can be browsed with a user interface module developed as an extension to Chimera, an extensible molecular modeling program. Features of the user interface module facilitate viewing multiple superpositions together. The SSD interface module can be downloaded from http://ssd.rbvi.ucsf.edu.