Open AccessHOMSTRAD: adding sequence information to structure-based alignments of homologous protein families
Author(s) -
Paul I. W. de Bakker,
Alex Bateman,
David F. Burke,
Ricardo Núñez Miguel,
Kenji Mizuguchi,
Jiye Shi,
Hiroki Shirai,
Tom L. Blundell
Publication year - 2001
Publication title -
bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.599
H-Index - 390
eISSN - 1367-4811
pISSN - 1367-4803
DOI - 10.1093/bioinformatics/17.8.748
Subject(s) - homology (biology) , sequence homology , homologous chromosome , sequence alignment , protein superfamily , structural alignment , sequence (biology) , homology modeling , computer science , computational biology , biology , genetics , database , peptide sequence , amino acid , base sequence , dna , gene , biochemistry , enzyme
summary: We describe an extension to the Homologous Structure Alignment Database (HOMSTRAD; Mizuguchi et al., Protein Sci., 7, 2469-2471, 1998a) to include homologous sequences derived from the protein families database Pfam (Bateman et al., Nucleic Acids Res., 28, 263-266, 2000). HOMSTRAD is integrated with the server FUGUE (Shi et al., submitted, 2001) for recognition and alignment of homologues, benefitting from the combination of abundant sequence information and accurate structure-based alignments. AVAILABILITY The HOMSTRAD database is available at: http://www-cryst.bioc.cam.ac.uk/homstrad/. Query sequences can be submitted to the homology recognition/alignment server FUGUE at: http://www-cryst.bioc.cam.ac.uk/fugue/.
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