MMDB: 3D structures and macromolecular interactions

被引：71

作者：

Madej, Thomas ^{[1
]}

Addess, Kenneth J. ^{[1
]}

Fong, Jessica H. ^{[1
]}

Geer, Lewis Y. ^{[1
]}

Geer, Renata C. ^{[1
]}

Lanczycki, Christopher J. ^{[1
]}

Liu, Chunlei ^{[1
]}

Lu, Shennan ^{[1
]}

Marchler-Bauer, Aron ^{[1
]}

Panchenko, Anna R. ^{[1
]}

Chen, Jie ^{[1
]}

Thiessen, Paul A. ^{[1
]}

Wang, Yanli ^{[1
]}

Zhang, Dachuan ^{[1
]}

Bryant, Stephen H. ^{[1
]}

机构：

[1] Natl Lib Med, Natl Ctr Biotechnol Informat, NIH, Bethesda, MD 20894 USA

来源：

NUCLEIC ACIDS RESEARCH | 2012年 / 40卷 / D1期

基金：

美国国家卫生研究院;

关键词：

D O I：

10.1093/nar/gkr1162

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：

Close to 60% of protein sequences tracked in comprehensive databases can be mapped to a known three-dimensional (3D) structure by standard sequence similarity searches. Potentially, a great deal can be learned about proteins or protein families of interest from considering 3D structure, and to this day 3D structure data may remain an underutilized resource. Here we present enhancements in the Molecular Modeling Database (MMDB) and its data presentation, specifically pertaining to biologically relevant complexes and molecular interactions. MMDB is tightly integrated with NCBI's Entrez search and retrieval system, and mirrors the contents of the Protein Data Bank. It links protein 3D structure data with sequence data, sequence classification resources and PubChem, a repository of small-molecule chemical structures and their biological activities, facilitating access to 3D structure data not only for structural biologists, but also for molecular biologists and chemists. MMDB provides a complete set of detailed and pre-computed structural alignments obtained with the VAST algorithm, and provides visualization tools for 3D structure and structure/sequence alignment via the molecular graphics viewer Cn3D. MMDB can be accessed at http://www.ncbi.nlm.nih.gov/structure.

引用

页码：D461 / D464

页数：4

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