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

J 2019

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

BURLEY, S.K., H.M. BERMAN, C. BHIKADIYA, C.X. BI, L. CHEN et. al.

Basic information

Original name

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

Authors

BURLEY, S.K. (840 United States of America), H.M. BERMAN (840 United States of America), C. BHIKADIYA (840 United States of America), C.X. BI (840 United States of America), L. CHEN (840 United States of America), L. DI COSTANZO (840 United States of America), C. CHRISTIE (840 United States of America), J.M. DUARTE (840 United States of America), S. DUTTA (840 United States of America), Z.K. FENG (840 United States of America), S. GHOSH (840 United States of America), D.S. GOODSELL (840 United States of America), R.K. GREEN (840 United States of America), V. GURANOVIC (840 United States of America), D. GUZENKO (840 United States of America), B.P. HUDSON (840 United States of America), Y.H. LIANG (840 United States of America), R. LOWE (840 United States of America), E. PEISACH (840 United States of America), I. PERISKOVA (840 United States of America), C. RANDLE (840 United States of America), A. ROSE (840 United States of America), M. SEKHARAN (840 United States of America), CH. SHAO (840 United States of America), Y.P. TAO (840 United States of America), Y. VALASATAVA (840 United States of America), M. VOIGT (840 United States of America), J. WESTBROOK (840 United States of America), J. YOUNG (840 United States of America), C. ZARDECKI (840 United States of America), M. ZHURAVLEVA (840 United States of America), G. KURISU (392 Japan), H. NAKAMURA (392 Japan), Y. KENGAKU (392 Japan), H. CHO (392 Japan), J. SATO (392 Japan), J.Y. KIM (392 Japan), Y. IKEGAWA (392 Japan), A. NAKAGAWA (392 Japan), R. YAMASHITA (392 Japan), T. KUDOU (392 Japan), G.J. BEKKER (392 Japan), H. SUZUKI (392 Japan), T. IWATA (392 Japan), M. YOKOCHI (392 Japan), N. KOBAYASHI (392 Japan), T. FUJIWARA (392 Japan), S. VELANKAR (826 United Kingdom of Great Britain and Northern Ireland), G.J. KLEYWEGT (826 United Kingdom of Great Britain and Northern Ireland), S. ANYANGO (826 United Kingdom of Great Britain and Northern Ireland), D.R. ARMSTRONG (826 United Kingdom of Great Britain and Northern Ireland), J.M. BERRISFORD (826 United Kingdom of Great Britain and Northern Ireland), M.J. CONROY (826 United Kingdom of Great Britain and Northern Ireland), J.M. DANA (826 United Kingdom of Great Britain and Northern Ireland), M. DESHPANDE (826 United Kingdom of Great Britain and Northern Ireland), P. GANE (826 United Kingdom of Great Britain and Northern Ireland), Romana GÁBOROVÁ (703 Slovakia, belonging to the institution), D. GUPTA (826 United Kingdom of Great Britain and Northern Ireland), A. GUTMANAS (826 United Kingdom of Great Britain and Northern Ireland), Jaroslav KOČA (203 Czech Republic, guarantor, belonging to the institution), L. MAK (826 United Kingdom of Great Britain and Northern Ireland), S. MIR (826 United Kingdom of Great Britain and Northern Ireland), A. MUKHOPADHYAY (826 United Kingdom of Great Britain and Northern Ireland), N. NADZIRIN (826 United Kingdom of Great Britain and Northern Ireland), S. NAIR (826 United Kingdom of Great Britain and Northern Ireland), A. PATWARDHAN (826 United Kingdom of Great Britain and Northern Ireland), T. PAYSAN-LAFOSSE (826 United Kingdom of Great Britain and Northern Ireland), Lukáš PRAVDA (203 Czech Republic), O. SALIH (826 United Kingdom of Great Britain and Northern Ireland), David SEHNAL (203 Czech Republic, belonging to the institution), M. VARADI (826 United Kingdom of Great Britain and Northern Ireland), Radka SVOBODOVÁ VAŘEKOVÁ (203 Czech Republic, belonging to the institution), J.L. MARKLEY (840 United States of America), J.C. HOCH (840 United States of America), P.R. ROMERO (840 United States of America), K. BASKARAN (840 United States of America), D. MAZIUK (840 United States of America), E.L. ULRICH (840 United States of America), J.R. WEDELL (840 United States of America), H.Y. YAO (840 United States of America), M. LIVNY (840 United States of America) and Y.E. IOANNIDIS (300 Greece)

Edition

Nucleic Acids Research, Oxford, Oxford University Press, 2019, 0305-1048

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 11.502

RIV identification code

RIV/00216224:14740/19:00109524

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1093/nar/gky949

UT WoS

000462587400074

Keywords in English

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

Abstract

V originále

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.

Links

90091, large research infrastructures

Name: NCMG

Citovat

BURLEY, S.K., H.M. BERMAN, C. BHIKADIYA, C.X. BI, L. CHEN, L. DI COSTANZO, C. CHRISTIE, J.M. DUARTE, S. DUTTA, Z.K. FENG, S. GHOSH, D.S. GOODSELL, R.K. GREEN, V. GURANOVIC, D. GUZENKO, B.P. HUDSON, Y.H. LIANG, R. LOWE, E. PEISACH, I. PERISKOVA, C. RANDLE, A. ROSE, M. SEKHARAN, CH. SHAO, Y.P. TAO, Y. VALASATAVA, M. VOIGT, J. WESTBROOK, J. YOUNG, C. ZARDECKI, M. ZHURAVLEVA, G. KURISU, H. NAKAMURA, Y. KENGAKU, H. CHO, J. SATO, J.Y. KIM, Y. IKEGAWA, A. NAKAGAWA, R. YAMASHITA, T. KUDOU, G.J. BEKKER, H. SUZUKI, T. IWATA, M. YOKOCHI, N. KOBAYASHI, T. FUJIWARA, S. VELANKAR, G.J. KLEYWEGT, S. ANYANGO, D.R. ARMSTRONG, J.M. BERRISFORD, M.J. CONROY, J.M. DANA, M. DESHPANDE, P. GANE, Romana GÁBOROVÁ, D. GUPTA, A. GUTMANAS, Jaroslav KOČA, L. MAK, S. MIR, A. MUKHOPADHYAY, N. NADZIRIN, S. NAIR, A. PATWARDHAN, T. PAYSAN-LAFOSSE, Lukáš PRAVDA, O. SALIH, David SEHNAL, M. VARADI, Radka SVOBODOVÁ VAŘEKOVÁ, J.L. MARKLEY, J.C. HOCH, P.R. ROMERO, K. BASKARAN, D. MAZIUK, E.L. ULRICH, J.R. WEDELL, H.Y. YAO, M. LIVNY and Y.E. IOANNIDIS. Protein Data Bank: the single global archive for 3D macromolecular structure data. Nucleic Acids Research. Oxford: Oxford University Press, 2019, vol. 47, D1, p. "D520"-"D528", 9 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gky949.

@article{1525776,
   author = {Burley, S.K. and Berman, H.M. and Bhikadiya, C. and Bi, C.X. and Chen, L. and Di Costanzo, L. and Christie, C. and Duarte, J.M. and Dutta, S. and Feng, Z.K. and Ghosh, S. and Goodsell, D.S. and Green, R.K. and Guranovic, V. and Guzenko, D. and Hudson, B.P. and Liang, Y.H. and Lowe, R. and Peisach, E. and Periskova, I. and Randle, C. and Rose, A. and Sekharan, M. and Shao, CH. and Tao, Y.P. and Valasatava, Y. and Voigt, M. and Westbrook, J. and Young, J. and Zardecki, C. and Zhuravleva, M. and Kurisu, G. and Nakamura, H. and Kengaku, Y. and Cho, H. and Sato, J. and Kim, J.Y. and Ikegawa, Y. and Nakagawa, A. and Yamashita, R. and Kudou, T. and Bekker, G.J. and Suzuki, H. and Iwata, T. and Yokochi, M. and Kobayashi, N. and Fujiwara, T. and Velankar, S. and Kleywegt, G.J. and Anyango, S. and Armstrong, D.R. and Berrisford, J.M. and Conroy, M.J. and Dana, J.M. and Deshpande, M. and Gane, P. and Gáborová, Romana and Gupta, D. and Gutmanas, A. and Koča, Jaroslav and Mak, L. and Mir, S. and Mukhopadhyay, A. and Nadzirin, N. and Nair, S. and Patwardhan, A. and PaysanandLafosse, T. and Pravda, Lukáš and Salih, O. and Sehnal, David and Varadi, M. and Svobodová Vařeková, Radka and Markley, J.L. and Hoch, J.C. and Romero, P.R. and Baskaran, K. and Maziuk, D. and Ulrich, E.L. and Wedell, J.R. and Yao, H.Y. and Livny, M. and Ioannidis, Y.E.},
   article_location = {Oxford},
   article_number = {D1},
   doi = {http://dx.doi.org/10.1093/nar/gky949},
   keywords = {RESOURCE DESCRIPTION FRAMEWORK; VALIDATION; REPRESENTATION; PREDICTION; DEPOSITION; CHALLENGE; SYSTEM; TOOLS},
   language = {eng},
   issn = {0305-1048},
   journal = {Nucleic Acids Research},
   title = {Protein Data Bank: the single global archive for 3D macromolecular structure data},
   url = {https://watermark.silverchair.com/gky949.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAkcwggJDBgkqhkiG9w0BBwagggI0MIICMAIBADCCAikGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMSCpWwcF1Ng8fBDIvAgEQgIIB-odjUWOo8vhiqdQgtXEv8-OFWQj5DEtz_zaYO_p6QkxzqK8},
   volume = {47},
   year = {2019}
}

TY  - JOUR
ID  - 1525776
AU  - Burley, S.K. - Berman, H.M. - Bhikadiya, C. - Bi, C.X. - Chen, L. - Di Costanzo, L. - Christie, C. - Duarte, J.M. - Dutta, S. - Feng, Z.K. - Ghosh, S. - Goodsell, D.S. - Green, R.K. - Guranovic, V. - Guzenko, D. - Hudson, B.P. - Liang, Y.H. - Lowe, R. - Peisach, E. - Periskova, I. - Randle, C. - Rose, A. - Sekharan, M. - Shao, CH. - Tao, Y.P. - Valasatava, Y. - Voigt, M. - Westbrook, J. - Young, J. - Zardecki, C. - Zhuravleva, M. - Kurisu, G. - Nakamura, H. - Kengaku, Y. - Cho, H. - Sato, J. - Kim, J.Y. - Ikegawa, Y. - Nakagawa, A. - Yamashita, R. - Kudou, T. - Bekker, G.J. - Suzuki, H. - Iwata, T. - Yokochi, M. - Kobayashi, N. - Fujiwara, T. - Velankar, S. - Kleywegt, G.J. - Anyango, S. - Armstrong, D.R. - Berrisford, J.M. - Conroy, M.J. - Dana, J.M. - Deshpande, M. - Gane, P. - Gáborová, Romana - Gupta, D. - Gutmanas, A. - Koča, Jaroslav - Mak, L. - Mir, S. - Mukhopadhyay, A. - Nadzirin, N. - Nair, S. - Patwardhan, A. - Paysan-Lafosse, T. - Pravda, Lukáš - Salih, O. - Sehnal, David - Varadi, M. - Svobodová Vařeková, Radka - Markley, J.L. - Hoch, J.C. - Romero, P.R. - Baskaran, K. - Maziuk, D. - Ulrich, E.L. - Wedell, J.R. - Yao, H.Y. - Livny, M. - Ioannidis, Y.E.
PY  - 2019
TI  - Protein Data Bank: the single global archive for 3D macromolecular structure data
JF  - Nucleic Acids Research
VL  - 47
IS  - D1
SP  - "D520"-"D528"
EP  - "D520"-"D528"
PB  - Oxford University Press
SN  - 03051048
KW  - RESOURCE DESCRIPTION FRAMEWORK
KW  - VALIDATION
KW  - REPRESENTATION
KW  - PREDICTION
KW  - DEPOSITION
KW  - CHALLENGE
KW  - SYSTEM
KW  - TOOLS
UR  - https://watermark.silverchair.com/gky949.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAkcwggJDBgkqhkiG9w0BBwagggI0MIICMAIBADCCAikGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMSCpWwcF1Ng8fBDIvAgEQgIIB-odjUWOo8vhiqdQgtXEv8-OFWQj5DEtz_zaYO_p6QkxzqK8
L2  - https://watermark.silverchair.com/gky949.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAkcwggJDBgkqhkiG9w0BBwagggI0MIICMAIBADCCAikGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMSCpWwcF1Ng8fBDIvAgEQgIIB-odjUWOo8vhiqdQgtXEv8-OFWQj5DEtz_zaYO_p6QkxzqK8
N2  - 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.
ER  -

BURLEY, S.K., H.M. BERMAN, C. BHIKADIYA, C.X. BI, L. CHEN, L. DI COSTANZO, C. CHRISTIE, J.M. DUARTE, S. DUTTA, Z.K. FENG, S. GHOSH, D.S. GOODSELL, R.K. GREEN, V. GURANOVIC, D. GUZENKO, B.P. HUDSON, Y.H. LIANG, R. LOWE, E. PEISACH, I. PERISKOVA, C. RANDLE, A. ROSE, M. SEKHARAN, CH. SHAO, Y.P. TAO, Y. VALASATAVA, M. VOIGT, J. WESTBROOK, J. YOUNG, C. ZARDECKI, M. ZHURAVLEVA, G. KURISU, H. NAKAMURA, Y. KENGAKU, H. CHO, J. SATO, J.Y. KIM, Y. IKEGAWA, A. NAKAGAWA, R. YAMASHITA, T. KUDOU, G.J. BEKKER, H. SUZUKI, T. IWATA, M. YOKOCHI, N. KOBAYASHI, T. FUJIWARA, S. VELANKAR, G.J. KLEYWEGT, S. ANYANGO, D.R. ARMSTRONG, J.M. BERRISFORD, M.J. CONROY, J.M. DANA, M. DESHPANDE, P. GANE, Romana GÁBOROVÁ, D. GUPTA, A. GUTMANAS, Jaroslav KOČA, L. MAK, S. MIR, A. MUKHOPADHYAY, N. NADZIRIN, S. NAIR, A. PATWARDHAN, T. PAYSAN-LAFOSSE, Lukáš PRAVDA, O. SALIH, David SEHNAL, M. VARADI, Radka SVOBODOVÁ VAŘEKOVÁ, J.L. MARKLEY, J.C. HOCH, P.R. ROMERO, K. BASKARAN, D. MAZIUK, E.L. ULRICH, J.R. WEDELL, H.Y. YAO, M. LIVNY and Y.E. IOANNIDIS. Protein Data Bank: the single global archive for 3D macromolecular structure data. \textit{Nucleic Acids Research}. Oxford: Oxford University Press, 2019, vol.~47, D1, p.~''D520''-''D528'', 9 pp. ISSN~0305-1048. Available from: https://dx.doi.org/10.1093/nar/gky949.

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