title: The HSSP database of protein structure-sequence alignments and family profiles.
abstract: 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.
authors.affiliation: European Bioinformatics Institute, EMBL-EBI, Genome Campus, Cambridge CB10 1SD, UK.
authors.forename: C
authors.initials: C
authors.lastname: Dodge
authors.forename: R
authors.initials: R
authors.lastname: Schneider
authors.forename: C
authors.initials: C
authors.lastname: Sander
mesh_terms: D003195:Computer Communication Networks; D016208:Databases, Factual; D016247:Information Storage and Retrieval; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment
chemical_list: D011506:Proteins