The HSSP database of protein structure-sequence alignments | Zendy

Reinhard Schneider | Zendy; Antoine de Daruvar | Zendy; Chris Sander | Zendy

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The HSSP database of protein structure-sequence alignments

Author(s) -

Reinhard Schneider,

Antoine de Daruvar,

Chris Sander

Publication year - 1997

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/25.1.226

Subject(s) - protein data bank (rcsb pdb) , biology , sequence database , database , sequence (biology) , protein data bank , sequence alignment , protein structure database , sequence logo , protein structure , peptide sequence , computational biology , genetics , computer science , biochemistry , gene

HSSP is a derived database merging structural (3-D) and sequence (1-D) information. For each protein of known 3-D structure from the Protein Data Bank (PDB), the database has a multiple sequence alignment of all available homologues and a sequence profile characteristic of the family. The list of homologues is the result of a database search in SwissProt using a position-weighted dynamic programming method for sequence profile alignment (MaxHom). The database is updated frequently. The listed homologues are very likely to have the same 3-D structure as the PDB protein to which they have been aligned. As a result, the database is not only a database of aligned sequence families, but also a database of implied secondary and tertiary structures covering 29% of all SwissProt-stored sequences.

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