DBAIi: a database of protein structure alignments

The DBAli database includes approximately 35 000 alignments of pairs of pro tein 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). DB Ali is linked to several resources, including Compare3D (Shindyalov and Bou rne, http://www.sdsc.edu/pb/software.htm, 1999) and ModView (Ilyin and Sali , http://guitar.rockefeller.edu/ModView/, 2001) for visualizing sequence al ignments and structure superpositions. A flexible search of DBAli by protei n sequence and structure properties allows construction of subsets of align ments suitable for a number of applications, such as benchmarking of sequen ce-sequence and sequence-structure alignment methods under a variety of con ditions.