DBAli: A Database of Protein Structure Alignments

Bioinformatics. 2001 Aug;17(8):746-7. doi: 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/

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Computational Biology
  • Databases, Protein*
  • Proteins / chemistry*
  • Proteins / genetics*
  • Sequence Alignment / statistics & numerical data*
  • Software
  • Software Design

Substances

  • Proteins