DBAli: a database of protein structure alignments

Open Access

1 August 2001

journal article
research article
Published by Oxford University Press (OUP) in Bioinformatics

Vol. 17 (8) , 746-747
https://doi.org/10.1093/bioinformatics/17.8.746

Abstract

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@rockefeller.edu; http://guitar.rockefeller.edu

Keywords

This publication has 3 references indexed in Scilit:

Threading a database of protein cores
Proteins-Structure Function and Bioinformatics, 1995
Derivation of rules for comparative protein modeling from a database of protein structure alignments
Protein Science, 1994
A data bank merging related protein structures and sequences
Protein Engineering, Design and Selection, 1992