蛋白质结构-序列比对与家族图谱的HSSP数据库。
The HSSP database of protein structure-sequence alignments and family profiles.
作者信息
Dodge C, Schneider R, Sander C
机构信息
European Bioinformatics Institute, EMBL-EBI, Genome Campus, Cambridge CB10 1SD, UK.
出版信息
Nucleic Acids Res. 1998 Jan 1;26(1):313-5. doi: 10.1093/nar/26.1.313.
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.
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本文引用的文献
1
Progress in protein structure prediction?
Trends Biochem Sci. 1993 Apr;18(4):120-3. doi: 10.1016/0968-0004(93)90017-h.
2
Protein structure comparison by alignment of distance matrices.
J Mol Biol. 1993 Sep 5;233(1):123-38. doi: 10.1006/jmbi.1993.1489.
3
PHD--an automatic mail server for protein secondary structure prediction.
Comput Appl Biosci. 1994 Feb;10(1):53-60. doi: 10.1093/bioinformatics/10.1.53.
4
A sequence property approach to searching protein databases.
J Mol Biol. 1995 Aug 18;251(3):390-9. doi: 10.1006/jmbi.1995.0442.
5
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.
Biopolymers. 1983 Dec;22(12):2577-637. doi: 10.1002/bip.360221211.
6
WHAT IF: a molecular modeling and drug design program.
J Mol Graph. 1990 Mar;8(1):52-6, 29. doi: 10.1016/0263-7855(90)80070-v.
7
Database of homology-derived protein structures and the structural meaning of sequence alignment.
Proteins. 1991;9(1):56-68. doi: 10.1002/prot.340090107.
8
The SWISS-PROT protein sequence data bank.
Nucleic Acids Res. 1992 May 11;20 Suppl(Suppl):2019-22. doi: 10.1093/nar/20.suppl.2019.
9
Fast and simple Monte Carlo algorithm for side chain optimization in proteins: application to model building by homology.
Proteins. 1992 Oct;14(2):213-23. doi: 10.1002/prot.340140208.
10
Selection of representative protein data sets.
Protein Sci. 1992 Mar;1(3):409-17. doi: 10.1002/pro.5560010313.
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