The HSSP database of protein structure sequence alignments and family profiles

Reference : The HSSP database of protein structure sequence alignments and family profiles


	Document type :	Scientific journals : Article
	Discipline(s) :	Life sciences : Biochemistry, biophysics & molecular biology
	To cite this reference:	http://hdl.handle.net/10993/26555

Title :	The HSSP database of protein structure sequence alignments and family profiles
Language :	English
Author, co-author :	Dodge, C. [> >]
	Schneider, Reinhard [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
	Sander, C. [> >]
Publication date :	1998
Journal title :	Nucleic Acids Research
Publisher :	Oxford University Press
Volume :	26
Issue/season :	1
Pages :	313-315
Peer reviewed :	Yes (verified by ORBi^lu)
ISSN :	0305-1048
e-ISSN :	1362-4962
City :	Oxford
Country :	United Kingdom
Abstract :	[en] 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.
Permalink :	http://hdl.handle.net/10993/26555
Other URL :	http://www.sander.embl-ebi.ac.uk/hssp/

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