Nucleic Acids Research, Vol 26, Issue 1 313-315, Copyright © 1998 by Oxford University Press
C Dodge, R Schneider and C Sander
HSSP (http: //www.sander.embl-ebi.ac.uk/hssp/) is a derived database
merging structure (3-D) and sequence (1-D) information. For each protein of
known 3D structure from the Protein Data Bank (PDB), we provide a multiple
sequence alignment of putative homologues and a sequence profile
characteristic of the protein family, centered on the known structure. The
list of homologues is the result of an iterative database search in
SWISS-PROT using a position-weighted dynamic programming method for
sequence profile alignment (MaxHom). The database is updated frequently.
The listed putative homologues are very likely to have the same 3D
structure as the PDB protein to which they have been aligned. As a result,
the database not only provides aligned sequence families, but also implies
secondary and tertiary structures covering 33% of all sequences in
SWISS-PROT.
ARTICLES
The HSSP database of protein structure-sequence alignments and family profiles
European Bioinformatics Institute, EMBL-EBI, Genome Campus, Cambridge CB10 1SD, UK.
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