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

Abstract

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.

Authors:
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Publication Date:
Research Org.:
Rutgers Univ., New Brunswick, NJ (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH); National Science Foundation (NSF)
Contributing Org.:
wwPDB Consortium
OSTI Identifier:
1479119
Alternate Identifier(s):
OSTI ID: 1600527
Grant/Contract Number:  
SC0019749; DBI-1338415
Resource Type:
Published Article
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Name: Nucleic Acids Research Journal Volume: 47 Journal Issue: D1; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Burley, Stephen K., Berman, Helen M., Bhikadiya, Charmi, Bi, Chunxiao, Chen, Li, Costanzo, Luigi Di, Christie, Cole, Duarte, Jose M., Dutta, Shuchismita, Feng, Zukang, Ghosh, Sutapa, Goodsell, David S., Green, Rachel Kramer, Guranovic, Vladimir, Guzenko, Dmytro, Hudson, Brian P., Liang, Yuhe, Lowe, Robert, Peisach, Ezra, Periskova, Irina, Randle, Chris, Rose, Alexander, Sekharan, Monica, Shao, Chenghua, Tao, Yi-Ping, Valasatava, Yana, Voigt, Maria, Westbrook, John, Young, Jasmine, Zardecki, Christine, Zhuravleva, Marina, Kurisu, Genji, Nakamura, Haruki, Kengaku, Yumiko, Cho, Hasumi, Sato, Junko, Kim, Ju Yaen, Ikegawa, Yasuyo, Nakagawa, Atsushi, Yamashita, Reiko, Kudou, Takahiro, Bekker, Gert-Jan, Suzuki, Hirofumi, Iwata, Takeshi, Yokochi, Masashi, Kobayashi, Naohiro, Fujiwara, Toshimichi, Velankar, Sameer, Kleywegt, Gerard J., Anyango, Stephen, Armstrong, David R., Berrisford, John M., Conroy, Matthew J., Dana, Jose M., Deshpande, Mandar, Gane, Paul, Gáborová, Romana, Gupta, Deepti, Gutmanas, Aleksandras, Koča, Jaroslav, Mak, Lora, Mir, Saqib, Mukhopadhyay, Abhik, Nadzirin, Nurul, Nair, Sreenath, Patwardhan, Ardan, Paysan-Lafosse, Typhaine, Pravda, Lukas, Salih, Osman, Sehnal, David, Varadi, Mihaly, Vařeková, Radka, Markley, John L., Hoch, Jeffrey C., Romero, Pedro R., Baskaran, Kumaran, Maziuk, Dimitri, Ulrich, Eldon L., Wedell, Jonathan R., Yao, Hongyang, Livny, Miron, and Ioannidis, Yannis E. Protein Data Bank: the single global archive for 3D macromolecular structure data. United Kingdom: N. p., 2018. Web. doi:10.1093/nar/gky949.
Burley, Stephen K., Berman, Helen M., Bhikadiya, Charmi, Bi, Chunxiao, Chen, Li, Costanzo, Luigi Di, Christie, Cole, Duarte, Jose M., Dutta, Shuchismita, Feng, Zukang, Ghosh, Sutapa, Goodsell, David S., Green, Rachel Kramer, Guranovic, Vladimir, Guzenko, Dmytro, Hudson, Brian P., Liang, Yuhe, Lowe, Robert, Peisach, Ezra, Periskova, Irina, Randle, Chris, Rose, Alexander, Sekharan, Monica, Shao, Chenghua, Tao, Yi-Ping, Valasatava, Yana, Voigt, Maria, Westbrook, John, Young, Jasmine, Zardecki, Christine, Zhuravleva, Marina, Kurisu, Genji, Nakamura, Haruki, Kengaku, Yumiko, Cho, Hasumi, Sato, Junko, Kim, Ju Yaen, Ikegawa, Yasuyo, Nakagawa, Atsushi, Yamashita, Reiko, Kudou, Takahiro, Bekker, Gert-Jan, Suzuki, Hirofumi, Iwata, Takeshi, Yokochi, Masashi, Kobayashi, Naohiro, Fujiwara, Toshimichi, Velankar, Sameer, Kleywegt, Gerard J., Anyango, Stephen, Armstrong, David R., Berrisford, John M., Conroy, Matthew J., Dana, Jose M., Deshpande, Mandar, Gane, Paul, Gáborová, Romana, Gupta, Deepti, Gutmanas, Aleksandras, Koča, Jaroslav, Mak, Lora, Mir, Saqib, Mukhopadhyay, Abhik, Nadzirin, Nurul, Nair, Sreenath, Patwardhan, Ardan, Paysan-Lafosse, Typhaine, Pravda, Lukas, Salih, Osman, Sehnal, David, Varadi, Mihaly, Vařeková, Radka, Markley, John L., Hoch, Jeffrey C., Romero, Pedro R., Baskaran, Kumaran, Maziuk, Dimitri, Ulrich, Eldon L., Wedell, Jonathan R., Yao, Hongyang, Livny, Miron, & Ioannidis, Yannis E. Protein Data Bank: the single global archive for 3D macromolecular structure data. United Kingdom. doi:10.1093/nar/gky949.
Burley, Stephen K., Berman, Helen M., Bhikadiya, Charmi, Bi, Chunxiao, Chen, Li, Costanzo, Luigi Di, Christie, Cole, Duarte, Jose M., Dutta, Shuchismita, Feng, Zukang, Ghosh, Sutapa, Goodsell, David S., Green, Rachel Kramer, Guranovic, Vladimir, Guzenko, Dmytro, Hudson, Brian P., Liang, Yuhe, Lowe, Robert, Peisach, Ezra, Periskova, Irina, Randle, Chris, Rose, Alexander, Sekharan, Monica, Shao, Chenghua, Tao, Yi-Ping, Valasatava, Yana, Voigt, Maria, Westbrook, John, Young, Jasmine, Zardecki, Christine, Zhuravleva, Marina, Kurisu, Genji, Nakamura, Haruki, Kengaku, Yumiko, Cho, Hasumi, Sato, Junko, Kim, Ju Yaen, Ikegawa, Yasuyo, Nakagawa, Atsushi, Yamashita, Reiko, Kudou, Takahiro, Bekker, Gert-Jan, Suzuki, Hirofumi, Iwata, Takeshi, Yokochi, Masashi, Kobayashi, Naohiro, Fujiwara, Toshimichi, Velankar, Sameer, Kleywegt, Gerard J., Anyango, Stephen, Armstrong, David R., Berrisford, John M., Conroy, Matthew J., Dana, Jose M., Deshpande, Mandar, Gane, Paul, Gáborová, Romana, Gupta, Deepti, Gutmanas, Aleksandras, Koča, Jaroslav, Mak, Lora, Mir, Saqib, Mukhopadhyay, Abhik, Nadzirin, Nurul, Nair, Sreenath, Patwardhan, Ardan, Paysan-Lafosse, Typhaine, Pravda, Lukas, Salih, Osman, Sehnal, David, Varadi, Mihaly, Vařeková, Radka, Markley, John L., Hoch, Jeffrey C., Romero, Pedro R., Baskaran, Kumaran, Maziuk, Dimitri, Ulrich, Eldon L., Wedell, Jonathan R., Yao, Hongyang, Livny, Miron, and Ioannidis, Yannis E. Wed . "Protein Data Bank: the single global archive for 3D macromolecular structure data". United Kingdom. doi:10.1093/nar/gky949.
@article{osti_1479119,
title = {Protein Data Bank: the single global archive for 3D macromolecular structure data},
author = {Burley, Stephen K. and Berman, Helen M. and Bhikadiya, Charmi and Bi, Chunxiao and Chen, Li and Costanzo, Luigi Di and Christie, Cole and Duarte, Jose M. and Dutta, Shuchismita and Feng, Zukang and Ghosh, Sutapa and Goodsell, David S. and Green, Rachel Kramer and Guranovic, Vladimir and Guzenko, Dmytro and Hudson, Brian P. and Liang, Yuhe and Lowe, Robert and Peisach, Ezra and Periskova, Irina and Randle, Chris and Rose, Alexander and Sekharan, Monica and Shao, Chenghua and Tao, Yi-Ping and Valasatava, Yana and Voigt, Maria and Westbrook, John and Young, Jasmine and Zardecki, Christine and Zhuravleva, Marina and Kurisu, Genji and Nakamura, Haruki and Kengaku, Yumiko and Cho, Hasumi and Sato, Junko and Kim, Ju Yaen and Ikegawa, Yasuyo and Nakagawa, Atsushi and Yamashita, Reiko and Kudou, Takahiro and Bekker, Gert-Jan and Suzuki, Hirofumi and Iwata, Takeshi and Yokochi, Masashi and Kobayashi, Naohiro and Fujiwara, Toshimichi and Velankar, Sameer and Kleywegt, Gerard J. and Anyango, Stephen and Armstrong, David R. and Berrisford, John M. and Conroy, Matthew J. and Dana, Jose M. and Deshpande, Mandar and Gane, Paul and Gáborová, Romana and Gupta, Deepti and Gutmanas, Aleksandras and Koča, Jaroslav and Mak, Lora and Mir, Saqib and Mukhopadhyay, Abhik and Nadzirin, Nurul and Nair, Sreenath and Patwardhan, Ardan and Paysan-Lafosse, Typhaine and Pravda, Lukas and Salih, Osman and Sehnal, David and Varadi, Mihaly and Vařeková, Radka and Markley, John L. and Hoch, Jeffrey C. and Romero, Pedro R. and Baskaran, Kumaran and Maziuk, Dimitri and Ulrich, Eldon L. and Wedell, Jonathan R. and Yao, Hongyang and Livny, Miron and Ioannidis, Yannis E.},
abstractNote = {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.},
doi = {10.1093/nar/gky949},
journal = {Nucleic Acids Research},
number = D1,
volume = 47,
place = {United Kingdom},
year = {2018},
month = {10}
}

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DOI: 10.1093/nar/gky949

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