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Bioinformatics Vol. 17 no. 8 2001
Pages 746-747
© 2001 Oxford University Press

Applications Note

DBAli: a database of protein structure alignments

Marc A. Martí-Renom , Valentin A. Ilyin and Andrej Sali *

Laboratories of Molecular Biophysics, Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, 1230 York Ave, New York, NY 10021, USA

Received on February 14, 2001 ; revised on April 25, 2001 ; accepted on April 25, 2001

Summary: The DBAli database includes approximately 35000 alignments of pairs of protein structures from SCOP (Lo Conte et al. , Nucleic Acids Res. , 28, 257–259, 2000) and CE (Shindyalov and Bourne, Protein Eng. , 11, 739–747, 1998). DBAli is linked to several resources, including Compare3D (Shindyalov and Bourne, http://www.sdsc.edu/pb/software.htm, 1999) and ModView (Ilyin and Sali, http://guitar.rockefeller.edu/ModView/, 2001) for visualizing sequence alignments and structure superpositions. A flexible search of DBAli by protein sequence and structure properties allows construction of subsets of alignments suitable for a number of applications, such as benchmarking of sequence–sequence and sequence–structure alignment methods under a variety of conditions.

Availability: http://guitar.rockefeller.edu/DBAli/

Contact: sali{at}rockefeller.edu; http://guitar.rockefeller.edu

* To whom correspondence should be addressed.


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