Protein Data Bank: the single global archive for 3D macromolecular structure data

被引：745

作者：

Burley, Stephen K. ^{[1
,2
,3
]}

Berman, Helen M. ^{[1
]}

Bhikadiya, Charmi ^{[1
]}

Bi, Chunxiao ^{[3
]}

Chen, Li ^{[1
]}

Di Costanzo, Luigi ^{[1
]}

Christie, Cole ^{[3
]}

Duarte, Jose M. ^{[3
]}

Dutta, Shuchismita ^{[1
]}

Feng, Zukang ^{[1
]}

Ghosh, Sutapa ^{[1
]}

Goodsell, David S. ^{[1
,4
]}

Green, Rachel Kramer ^{[1
]}

Guranovic, Vladimir ^{[1
]}

Guzenko, Dmytro ^{[2
]}

Hudson, Brian P. ^{[1
]}

Liang, Yuhe ^{[1
]}

Lowe, Robert ^{[1
]}

Peisach, Ezra ^{[1
]}

Periskova, Irina ^{[1
]}

Randle, Chris ^{[3
]}

Rose, Alexander ^{[3
]}

Sekharan, Monica ^{[1
]}

Shao, Chenghua ^{[1
]}

Tao, Yi-Ping ^{[1
]}

Valasatava, Yana ^{[3
]}

Voigt, Maria ^{[1
]}

Westbrook, John ^{[1
]}

Young, Jasmine ^{[1
]}

Zardecki, Christine ^{[1
]}

Zhuravleva, Marina ^{[1
]}

Kurisu, Genji ^{[5
]}

Nakamura, Haruki ^{[5
]}

Kengaku, Yumiko ^{[5
]}

Cho, Hasumi ^{[5
]}

Sato, Junko ^{[5
]}

Kim, Ju Yaen ^{[5
]}

Ikegawa, Yasuyo ^{[5
]}

Nakagawa, Atsushi ^{[5
]}

Yamashita, Reiko ^{[5
]}

Kudou, Takahiro ^{[5
]}

Bekker, Gert-Jan ^{[5
]}

Suzuki, Hirofumi ^{[5
]}

Iwata, Takeshi ^{[5
]}

Yokochi, Masashi ^{[5
]}

Kobayashi, Naohiro ^{[5
]}

Fujiwara, Toshimichi ^{[5
]}

Velankar, Sameer ^{[6
]}

Kleywegt, Gerard J. ^{[6
]}

Anyango, Stephen ^{[6
]}

机构：

[1] Rutgers State Univ, Res Collaboratory Struct Bioinformat Prot Data Ba, Inst Quantitat Biomed, Piscataway, NJ 08854 USA

[2] Univ Calif San Diego, Res Collaboratory Struct Bioinformat ProteinData, San Diego Supercomp Ctr, La Jolla, CA 92093 USA

[3] Univ Med & Dent New Jersey, Rutgers Canc Inst New Jersey, New Brunswick, NJ 08903 USA

[4] Scripps Res Inst, La Jolla, CA 92037 USA

[5] Osaka Univ, Inst Prot Res, Suita, Osaka 5650871, Japan

[6] EBI, Prot Data Bank Europe, EMBL, Wellcome Genome Campus, Cambridge CB10 1SD, England

[7] Masaryk Univ Brno, CEITEC Cent European Inst Technol, Kamencie 5, Brno 62500, Czech Republic

[8] EBI, Cellular Struct & 3D Bioimaging, EMBL, Wellcome Genome Campus, Cambridge CB10 1SD, England

[9] Univ Wisconsin, Biochem Dept, Madison, WI 53706 USA

[10] UConn Hlth, Dept Mol Biol & Biophys, Farmington, CT 06030 USA

[11] Univ Wisconsin, Dept Comp Sci, 1210 W Dayton St, Madison, WI 53706 USA

[12] ATHENA Res & Innovat Ctr, Athens, Greece

来源：

NUCLEIC ACIDS RESEARCH | 2019年 / 47卷 / D1期

基金：

美国国家科学基金会; 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; 美国国家卫生研究院;

关键词：

RESOURCE DESCRIPTION FRAMEWORK; VALIDATION; REPRESENTATION; PREDICTION; DEPOSITION; CHALLENGE; SYSTEM; TOOLS;

D O I：

10.1093/nar/gky949

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 single global archive of experimentally determined three-dimensional (3D) structure data of biological macromolecules. Since 2003, the PDB has been managed by the Worldwide Protein Data Bank (wwPDB; wwpdb.org), an international consortium that collaboratively oversees deposition, validation, biocuration, and open access dissemination of 3D macromolecular structure data. The PDB Core Archive houses 3D atomic coordinates of more than 144 000 structural models of proteins, DNA/RNA, and their complexes with metals and small molecules and related experimental data and metadata. Structure and experimental data/metadata are also stored in the PDB Core Archive using the readily extensible wwPDB PDBx/mmCIF master data format, which will continue to evolve as data/metadata from new experimental techniques and structure determination methods are incorporated by the wwPDB. Impacts of the recently developed universal wwPDB OneDep deposition/validation/biocuration system and various methods-specific wwPDB Validation Task Forces on improving the quality of structures and data housed in the PDB Core Archive are described together with current challenges and future plans.

引用

页码：D520 / D528

页数：9

共 42 条

[1]

Abbott S., 2018, CURR PROTOC BIOINFOR, V61

[2] Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop [J].

Adams, Paul D. ;

Aertgeerts, Kathleen ;

Bauer, Cary ;

Bell, Jeffrey A. ;

Berman, Helen M. ;

Bhat, Talapady N. ;

Blaney, Jeff M. ;

Bolton, Evan ;

Bricogne, Gerard ;

Brown, David ;

Burley, Stephen K. ;

Case, David A. ;

Clark, Kirk L. ;

Darden, Tom ;

Emsley, Paul ;

Feher, Victoria A. ;

Feng, Zukang ;

Groom, Colin R. ;

Harris, Seth F. ;

Hendle, Jorg ;

Holder, Thomas ;

Joachimiak, Andrzej ;

Kleywegt, Gerard J. ;

Krojer, Tobias ;

Marcotrigiano, Joseph ;

Mark, Alan E. ;

Markley, John L. ;

Miller, Matthew ;

Minor, Wladek ;

Montelione, Gaetano T. ;

Murshudov, Garib ;

Nakagawa, Atsushi ;

Nakamura, Haruki ;

Nicholls, Anthony ;

Nicklaus, Marc ;

Nolte, Robert T. ;

Padyana, Anil K. ;

Peishoff, Catherine E. ;

Pieniazek, Susan ;

Read, Randy J. ;

Shao, Chenghua ;

Sheriff, Steven ;

Smart, Oliver ;

Soisson, Stephen ;

Spurlino, John ;

Stouch, Terry ;

Svobodova, Radka ;

Tempel, Wolfram ;

Terwilliger, Thomas C. ;

Tronrud, Dale .

STRUCTURE, 2016, 24 (04) :502-508

[3]

[Anonymous], 1971, NATURE-NEW BIOL, V233, P223

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

Berman, H ;

Henrick, K ;

Nakamura, H .

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

[5] 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

[6] PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models [J].

Burley, Stephen K. ;

Kurisu, Genji ;

Markley, John L. ;

Nakamura, Haruki ;

Velankar, Sameer ;

Berman, Helen M. ;

Sali, Andrej ;

Schwede, Torsten ;

Trewhella, Jill .

STRUCTURE, 2017, 25 (09) :1317-1318

[7] BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank [J].

Doreleijers, JF ;

Mading, S ;

Maziuk, D ;

Sojourner, K ;

Yin, L ;

Zhu, J ;

Markley, JL ;

Ulrich, EL .

JOURNAL OF BIOMOLECULAR NMR, 2003, 26 (02) :139-146

[8]

Fitzgerald PMD, 2005, International Tables for Crystallography G. Definition and exchange of crystallographic data, P295

[9] D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies [J].

Gaieb, Zied ;

Liu, Shuai ;

Gathiaka, Symon ;

Chiu, Michael ;

Yang, Huanwang ;

Shao, Chenghua ;

Feher, Victoria A. ;

Walters, W. Patrick ;

Kuhn, Bernd ;

Rudolph, Markus G. ;

Burley, Stephen K. ;

Gilson, Michael K. ;

Amaro, Rommie E. .

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 2018, 32 (01) :1-20

[10] Validation of Structures in the Protein Data Bank [J].

Gore, Swanand ;

Garcia, Eduardo Sanz ;

Hendrickx, Pieter M. S. ;

Gutmanas, Aleksandras ;

Westbrook, John D. ;

Yang, Huanwang ;

Feng, Zukang ;

Baskaran, Kumaran ;

Berrisford, John M. ;

Hudson, Brian P. ;

Ikegawa, Yasuyo ;

Kobayashi, Naohiro ;

Lawson, Catherine L. ;

Mading, Steve ;

Mak, Lora ;

Mukhopadhyay, Abhik ;

Oldfield, Thomas J. ;

Patwardhan, Ardan ;

Peisach, Ezra ;

Sahni, Gaurav ;

Sekharan, Monica R. ;

Sen, Sanchayita ;

Shao, Chenghua ;

Smart, Oliver S. ;

Ulrich, Eldon L. ;

Yamashita, Reiko ;

Quesada, Martha ;

Young, Jasmine Y. ;

Nakamura, Haruki ;

Markley, John L. ;

Berman, Helen M. ;

Burley, Stephen K. ;

Velankar, Sameer ;

Kleywegt, Gerard J. .

STRUCTURE, 2017, 25 (12) :1916-1927

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