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：

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

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

[1] The universal protein resource (UniProt) [J].

Bairoch, Amos ;

Bougueleret, Lydie ;

Altairac, Severine ;

Amendolia, Valeria ;

Auchincloss, Andrea ;

Puy, Ghislaine Argoud ;

Axelsen, Kristian ;

Baratin, Delphine ;

Blatter, Marie-Claude ;

Boeckmann, Brigitte ;

Bollondi, Laurent ;

Boutet, Emmanuel ;

Quintaje, Silvia Braconi ;

Breuza, Lionel ;

Bridge, Alan ;

deCastro, Edouard ;

Coral, Danielle ;

Coudert, Elisabeth ;

Cusin, Isabelle ;

Dobrokhotov, Pavel ;

Dornevil, Dolnide ;

Duvaud, Severine ;

Estreicher, Anne ;

Famiglietti, Livia ;

Feuermann, Marc ;

Gehant, Sebastian ;

Farriol-Mathis, Nathalie ;

Ferro, Serenella ;

Gasteiger, Elisabeth ;

Gateau, Alain ;

Gerritsen, Vivienne ;

Gos, Arnaud ;

Gruaz-Gumowski, Nadine ;

Hinz, Ursula ;

Hulo, Chantal ;

Hulo, Nicolas ;

Ioannidis, Vassilios ;

Ivanyi, Ivan ;

James, Janet ;

Jain, Eric ;

Jimenez, Silvia ;

Jungo, Florence ;

Junker, Vivien ;

Keller, Guillaume ;

Lachaize, Corinne ;

Lane-Guermonprez, Lydie ;

Langendijk-Genevaux, Petra ;

Lara, Vicente ;

Lemercier, Philippe ;

Le Saux, Virginie .

NUCLEIC ACIDS RESEARCH, 2007, 35 :D193-D197

[2]

Benson DA, 2017, NUCLEIC ACIDS RES, V45, pD37, DOI [10.1093/nar/gkl986, 10.1093/nar/gkw1070, 10.1093/nar/gkg057, 10.1093/nar/gks1195, 10.1093/nar/gkp1024, 10.1093/nar/gkq1079, 10.1093/nar/gkr1202, 10.1093/nar/gkx1094, 10.1093/nar/gkn723]

[3] Announcing the worldwide Protein Data Bank [J].

Berman, H ;

Henrick, K ;

Nakamura, H .

NATURE STRUCTURAL BIOLOGY, 2003, 10 (12) :980-980

[4] The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data [J].

Berman, Helen ;

Henrick, Kim ;

Nakamura, Haruki ;

Markley, John L. .

NUCLEIC ACIDS RESEARCH, 2007, 35 :D301-D303

[5] Outcome of a workshop on archiving structural models of biological macromolecules [J].

Berman, Helen M. ;

Burley, Stephen K. ;

Chiu, Wah ;

Sali, Andrej ;

Adzhubei, Alexel ;

Bourne, Philip E. ;

Bryant, Stephen H. ;

Dunbrack, Roland L., Jr. ;

Fidelis, Krzysztof ;

Frank, Joachim ;

Godzik, Adam ;

Henrick, Kim ;

Joachimiak, Andrzej ;

Heymann, Bernard ;

Jones, David ;

Markley, John L. ;

Moult, John ;

Montelione, Gaetano T. ;

Orengo, Christine ;

Rossmann, Michael G. ;

Rost, Burkhard ;

Saibil, Helen ;

Schwede, Torsten ;

Standley, Daron M. ;

Westbrook, John D. .

STRUCTURE, 2006, 14 (08) :1211-1217

[6] The Protein Data Bank [J].

Berman, HM ;

Westbrook, J ;

Feng, Z ;

Gilliland, G ;

Bhat, TN ;

Weissig, H ;

Shindyalov, IN ;

Bourne, PE .

NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :235-242

[7] PROTEIN DATA BANK - COMPUTER-BASED ARCHIVAL FILE FOR MACROMOLECULAR STRUCTURES [J].

BERNSTEIN, FC ;

KOETZLE, TF ;

WILLIAMS, GJB ;

MEYER, EF ;

BRICE, MD ;

RODGERS, JR ;

KENNARD, O ;

SHIMANOUCHI, T ;

TASUMI, M .

JOURNAL OF MOLECULAR BIOLOGY, 1977, 112 (03) :535-542

[8] Macromolecular crystallographic information file [J].

Bourne, PE ;

Berman, HM ;

McMahon, B ;

Watenpaugh, KD ;

Westbrook, JD ;

Fitzgerald, PMD .

MACROMOLECULAR CRYSTALLOGRAPHY, PT B, 1997, 277 :571-590

[9] Isolation and characterization of novel cyclotides from Viola hederaceae -: Solution structure and anti-HIV activity of vhl-1, a leaf-specific expressed cyclotide [J].

Chen, B ;

Colgrave, ML ;

Daly, NL ;

Rosengren, KJ ;

Gustafson, KR ;

Craik, DJ .

JOURNAL OF BIOLOGICAL CHEMISTRY, 2005, 280 (23) :22395-22405

[10] TargetDB: a target registration database for structural genomics projects [J].

Chen, L ;

Oughtred, R ;

Berman, HM ;

Westbrook, J .

BIOINFORMATICS, 2004, 20 (16) :2860-2862

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