A series of PDB related databases for everyday needs

被引：562

作者：

Joosten, Robbie P. ^{[2
]}

Beek, Tim A. H. Te ^{[1
]}

Krieger, Elmar ^{[1
]}

Hekkelman, Maarten L. ^{[1
]}

Hooft, Rob W. W. ^{[3
]}

Schneider, Reinhard ^{[4
]}

Sander, Chris ^{[5
]}

Vriend, Gert ^{[1
]}

机构：

[1] Radboud Univ Nijmegen Med Ctr, NCMLS 260, Ctr Mol & Biomol Informat, NL-6525 GA Nijmegen, Netherlands

[2] Netherlands Canc Inst, Dept Biochem, NL-1066 CX Amsterdam, Netherlands

[3] Netherlands Bioinformat Ctr, NL-6525 GA Nijmegen, Netherlands

[4] European Mol Biol Lab, D-69117 Heidelberg, Germany

[5] Mem Sloan Kettering Canc Ctr, Computat Biol Ctr, New York, NY 10065 USA

来源：

NUCLEIC ACIDS RESEARCH | 2011年 / 39卷

基金：

美国国家卫生研究院;

关键词：

PROTEIN DATA-BANK; SECONDARY STRUCTURE; HSSP DATABASE; CRYSTAL-STRUCTURE; RETRIEVAL-SYSTEM; REFINEMENT; PARAMETERS; MOLECULES; MODELS; CLASSIFICATION;

D O I：

10.1093/nar/gkq1105

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The Protein Data Bank (PDB) is the world-wide repository of macromolecular structure information. We present a series of databases that run parallel to the PDB. Each database holds one entry, if possible, for each PDB entry. DSSP holds the secondary structure of the proteins. PDBREPORT holds reports on the structure quality and lists errors. HSSP holds a multiple sequence alignment for all proteins. The PDBFINDER holds easy to parse summaries of the PDB file content, augmented with essentials from the other systems. PDB_REDO holds re-refined, and often improved, copies of all structures solved by X-ray. WHY_NOT summarizes why certain files could not be produced. All these systems are updated weekly. The data sets can be used for the analysis of properties of protein structures in areas ranging from structural genomics, to cancer biology and protein design.

引用

页码：D411 / D419

页数：9

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