The Protein Data Bank archive as an open data resource

被引：90

作者：

Berman, Helen M. ^{[1
,2
]}

Kleywegt, Gerard J. ^{[3
]}

Nakamura, Haruki ^{[4
]}

Markley, John L. ^{[5
]}

机构：

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

[2] Rutgers State Univ, Ctr Integrat Prote Res, Piscataway, NJ 08854 USA

[3] European Bioinformat Inst, European Mol Biol Lab, PDBe, Cambridge CB10 1SD, England

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

[5] Univ Wisconsin, Dept Biochem, BioMagResBank, Madison, WI 53706 USA

来源：

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN | 2014年 / 28卷 / 10期

基金：

英国生物技术与生命科学研究理事会; 英国惠康基金; 美国国家科学基金会;

关键词：

Protein Data Bank; Protein structure; Biomacromolecules; Data archive; 3-DIMENSIONAL FOURIER SYNTHESIS; CRYSTAL-STRUCTURE; RIBOSOMAL-SUBUNIT; STRUCTURAL CLASSIFICATION; ATOMIC-STRUCTURE; BINDING; WWPDB; MYOGLOBIN; INSULIN; PDBSUM;

D O I：

10.1007/s10822-014-9770-y

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 archive was established in 1971, and recently celebrated its 40th anniversary (Berman et al. in Structure 20:391, 2012). An analysis of interrelationships of the science, technology and community leads to further insights into how this resource evolved into one of the oldest and most widely used open-access data resources in biology.

引用

页码：1009 / 1014

页数：6

共 61 条

[51] CRYSTAL-STRUCTURE OF TRP REPRESSOR OPERATOR COMPLEX AT ATOMIC RESOLUTION [J].

OTWINOWSKI, Z ;

SCHEVITZ, RW ;

ZHANG, RG ;

LAWSON, CL ;

JOACHIMIAK, A ;

MARMORSTEIN, RQ ;

LUISI, BF ;

SIGLER, PB .

NATURE, 1988, 335 (6188) :321-329

[52] STRUCTURE OF HAEMOGLOBIN - 3-DIMENSIONAL FOURIER SYNTHESIS AT 5.5-A RESOLUTION, OBTAINED BY X-RAY ANALYSIS [J].

PERUTZ, MF ;

ROSSMANN, MG ;

CULLIS, AF ;

MUIRHEAD, H ;

WILL, G ;

NORTH, ACT .

NATURE, 1960, 185 (4711) :416-422

[53] The wwPDB common tool for deposition and annotation [J].

Quesada, Martha ;

Westbrook, John ;

Oldfield, Tom ;

Young, Jasmine ;

Swaminathan, Jawahar ;

Feng, Zukang ;

Velankar, Sameer ;

Matsuura, Takanori ;

Ulrich, Eldon ;

Madding, Steve ;

Kleywegt, Gerard J. ;

Markley, John L. ;

Nakamura, Haruki ;

Berman, Helen M. .

ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES, 2011, 67 :C403-C404

[54] A New Generation of Crystallographic Validation Tools for the Protein Data Bank [J].

Read, Randy J. ;

Adams, Paul D. ;

Arendall, W. Bryan, III ;

Brunger, Axel T. ;

Emsley, Paul ;

Joosten, Robbie P. ;

Kleywegt, Gerard J. ;

Krissinel, Eugene B. ;

Luetteke, Thomas ;

Otwinowski, Zbyszek ;

Perrakis, Anastassis ;

Richardson, Jane S. ;

Sheffler, William H. ;

Smith, Janet L. ;

Tickle, Ian J. ;

Vriend, Gert ;

Zwart, Peter H. .

STRUCTURE, 2011, 19 (10) :1395-1412

[55] Structure of functionally activated small ribosomal subunit at 3.3 Å resolution [J].

Schluenzen, F ;

Tocilj, A ;

Zarivach, R ;

Harms, J ;

Gluehmann, M ;

Janell, D ;

Bashan, A ;

Bartels, H ;

Agmon, I ;

Franceschi, F ;

Yonath, A .

CELL, 2000, 102 (05) :615-623

[56] CRYSTAL-STRUCTURE OF YEAST PHENYLALANINE TRANSFER-RNA .1. CRYSTALLOGRAPHIC REFINEMENT [J].

SUSSMAN, JL ;

HOLBROOK, SR ;

WARRANT, RW ;

CHURCH, GM ;

KIM, SH .

JOURNAL OF MOLECULAR BIOLOGY, 1978, 123 (04) :607-630

[57] BioMagResBank [J].

Ulrich, Eldon L. ;

Akutsu, Hideo ;

Doreleijers, Jurgen F. ;

Harano, Yoko ;

Ioannidis, Yannis E. ;

Lin, Jundong ;

Livny, Miron ;

Mading, Steve ;

Maziuk, Dimitri ;

Miller, Zachary ;

Nakatani, Eiichi ;

Schulte, Christopher F. ;

Tolmie, David E. ;

Wenger, R. Kent ;

Yao, Hongyang ;

Markley, John L. .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D402-D408

[58] The PDBbind database: Methodologies and updates [J].

Wang, RX ;

Fang, XL ;

Lu, YP ;

Yang, CY ;

Wang, SM .

JOURNAL OF MEDICINAL CHEMISTRY, 2005, 48 (12) :4111-4119

[59]

Westbrook JD, 2005, International Tables for Crystallography, P195

[60] The crystal structure of the asymmetric GroEL-GroES-(ADP)(7) chaperonin complex [J].

Xu, ZH ;

Horwich, AL ;

Sigler, PB .

NATURE, 1997, 388 (6644) :741-750

← 1 2 3 4 5 6 7 →