Data Deposition and Annotation at the Worldwide Protein Data Bank

被引：87

作者：

Dutta, Shuchismita ^{[1
]}

Burkhardt, Kyle ^{[1
]}

Young, Jasmine ^{[1
]}

Swaminathan, Ganesh J. ^{[2
]}

Matsuura, Takanori ^{[3
]}

Henrick, Kim ^{[2
]}

Nakamura, Haruki ^{[3
]}

Berman, Helen M. ^{[1
]}

机构：

[1] Rutgers State Univ, RCSB PDB, Dept Chem & Chem Biol, Piscataway, NJ 08854 USA

[2] EMBL Outstn Hinxton, Macromol Struct Database European Bioinformat Ins, Cambridge CB10 1SD, England

[3] Osaka Univ, PDBj, Inst Prot Res, Suita, Osaka 5650871, Japan

来源：

MOLECULAR BIOTECHNOLOGY | 2009年 / 42卷 / 01期

基金：

美国国家科学基金会; 英国医学研究理事会; 英国惠康基金; 英国生物技术与生命科学研究理事会; 日本科学技术振兴机构;

关键词：

Protein Data Bank (PDB); wwPDB; Deposition; Annotation; Validation; E-MSD; SYSTEM; VALIDATION; MANAGEMENT; RESOURCE; ARCHIVE; CACTVS;

D O I：

10.1007/s12033-008-9127-7

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 repository for three-dimensional structures of biological macromolecules, determined by experimental methods. The data in the archive is free and easily available via the Internet from any of the worldwide centers managing this global archive. These data are used by scientists, researchers, bioinformatics specialists, educators, students, and general audiences to understand biological phenomenon at a molecular level. Analysis of this structural data also inspires and facilitates new discoveries in science. This chapter describes the tools and methods currently used for deposition, processing, and release of data in the PDB. References to future enhancements are also included.

引用

页码：1 / 13

页数：13

共 50 条

[31] The evolution of the Protein Data Bank
Berman, Helen M.
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 2011, 18 (12) : 1310 - 1310
[32] The membrane protein data bank
Raman, P
Cherezov, V
Caffrey, M
CELLULAR AND MOLECULAR LIFE SCIENCES, 2006, 63 (01) : 36 - 51
[33] The Future of the Protein Data Bank
Berman, Helen M.
Kleywegt, Gerard J.
Nakamura, Haruki
Markley, John L.
BIOPOLYMERS, 2013, 99 (03) : 218 - 222
[34] The Membrane Protein Data Bank
P. Raman
V. Cherezov
M. Caffrey
Cellular and Molecular Life Sciences, 2006, 63 : 36 - 51
[35] Trendspotting in the Protein Data Bank
Berman, Helen M.
Narayanan, Buvaneswari Coimbatore
Di Costanzo, Luigi
Dutta, Shuchismita
Ghosh, Sutapa
Hudson, Brian P.
Lawson, Catherine L.
Peisach, Ezra
Prlic, Andreas
Rose, Peter W.
Shao, Chenghua
Yang, Huanwang
Young, Jasmine
Zardecki, Christine
FEBS LETTERS, 2013, 587 (08) : 1036 - 1045
[36] The Protein Data Bank archive as an open data resource
Helen M. Berman
Gerard J. Kleywegt
Haruki Nakamura
John L. Markley
Journal of Computer-Aided Molecular Design, 2014, 28 : 1009 - 1014
[37] Protein Circular Dichroism Data Bank (PCDDB): Data bank and website design
Whitmore, Lee
Janes, Robert W.
Wallace, B. A.
CHIRALITY, 2006, 18 (06) : 426 - 429
[38] THE PROTEIN DATA BANK: DATA DISTRIBUTION AND QUERY FUNCTIONALITY
Bluhm, W. F.
Battistuz, T.
Clingman, E.
Deshpande, N.
Fleri, W.
Greer, D. S.
Padilla, D.
Stoner, D.
Weissig, H.
Bourne, P. E.
ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES, 2002, 58 : C214 - C214
[39] Data mining the protein data bank: Residue interactions
Oldfield, TJ
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2002, 49 (04) : 510 - 528
[40] The Protein Data Bank archive as an open data resource
Berman, Helen M.
Kleywegt, Gerard J.
Nakamura, Haruki
Markley, John L.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 2014, 28 (10) : 1009 - 1014

← 1 2 3 4 5 →