PDBe-KB: a community-driven resource for structural and
functional annotations

J 2020

PDBe-KB: a community-driven resource for structural and functional annotations

VARADI, Mihaly, John BCRRISFORD, Mandar DESHPANDE, Sreenath S. NAIR, Aleksandras GUTMANAS et. al.

Basic information

Original name

PDBe-KB: a community-driven resource for structural and functional annotations

Authors

VARADI, Mihaly, John BCRRISFORD, Mandar DESHPANDE, Sreenath S. NAIR, Aleksandras GUTMANAS, David ARMSTRONG, Lukáš PRAVDA, Bissan AL-LAZIKANI, Stephen ANYANGO, Geoffrey J. BARTON, Karel BERKA, Tom BLUNDELL, Neera BORKAKOTI, Jose DANA, Sayoni DAS, Sucharita DEY, Patrizio DI MICCO, Franca FRATERNALI, Toby GIBSON, Manuela HELMER-CITTERICH, David HOKSZA, Liang-Chin HUANG, Rishabh JAIN, Harry JUBB, Christos KANNAS, Natarajan KANNAN, Jaroslav KOČA (203 Czech Republic, belonging to the institution), Radoslav KRIVAK, Manjeet KUMAR, Emanuel D. LEVY, F. MADEIRA, M. S. MADHUSUDHAN, Henry J. MARTELL, Stuart MACGOWAN, Jake E. MCGREIG, Saqib MIR, Abhik MUKHOPADHYAY, Luca PARCA, Typhaine PAYSAN-LAFOSSE, Leandro RADUSKY, Antonio RIBEIRO, Luis SERRANO, Ian SILLITOE, Gulzar SINGH, Petr SKODA, Radka SVOBODOVÁ (203 Czech Republic, belonging to the institution), Jonathan TYZACK, Alfonso VALENCIA, Eloy Villasclaras FERNANDEZ, Wim VRANKEN, Mark WASS, Janet THORNTON, Michael STERNBERG, Christine ORENGO and Sameer VELANKAR

Edition

Nucleic acids research, Oxford, Oxford University Press, 2020, 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: 16.971

RIV identification code

RIV/00216224:14740/20:00117896

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1093/nar/gkz853

UT WoS

000525956700048

Keywords in English

PDBe-KB

Abstract

V originále

The Protein Data Bank in Europe-Knowledge Base (PDBe-KB, https://pdbe-kb.org) is a community-driven, collaborative resource for literature-derived, manually curated and computationally predicted structural and functional annotations of macro-molecular structure data, contained in the Protein Data Bank (PDB). The goal of PDBe-KB is two-fold: (i) to increase the visibility and reduce the fragmentation of annotations contributed by specialist data resources, and to make these data more findable, accessible, interoperable and reusable (FAIR) and (ii) to place macromolecular structure data in their biological context, thus facilitating their use by the broader scientific community in fundamental and applied research. Here, we describe the guidelines of this collaborative effort, the current status of contributed data, and the PDBe-KB infrastructure, which includes the data exchange format, the deposition system for added value annotations, the distributable database containing the assembled data, and programmatic access endpoints. We also describe a series of novel web-pages-the PDBe-KB aggregated views of structure data-which combine information on macromolecular structures from many PDB entries. We have recently released the first set of pages in this series, which provide an overview of available structural and functional information for a protein of interest, referenced by a UniProtKB accession.

Links

EF16_013/0001777, research and development project

Name: ELIXIR-CZ: Budování kapacit

LM2015047, research and development project

Name: Česká národní infrastruktura pro biologická data (Acronym: ELIXIR-CZ)

Investor: Ministry of Education, Youth and Sports of the CR, Czech National Infrastructure for Biological Data

Citovat

VARADI, Mihaly, John BCRRISFORD, Mandar DESHPANDE, Sreenath S. NAIR, Aleksandras GUTMANAS, David ARMSTRONG, Lukáš PRAVDA, Bissan AL-LAZIKANI, Stephen ANYANGO, Geoffrey J. BARTON, Karel BERKA, Tom BLUNDELL, Neera BORKAKOTI, Jose DANA, Sayoni DAS, Sucharita DEY, Patrizio DI MICCO, Franca FRATERNALI, Toby GIBSON, Manuela HELMER-CITTERICH, David HOKSZA, Liang-Chin HUANG, Rishabh JAIN, Harry JUBB, Christos KANNAS, Natarajan KANNAN, Jaroslav KOČA, Radoslav KRIVAK, Manjeet KUMAR, Emanuel D. LEVY, F. MADEIRA, M. S. MADHUSUDHAN, Henry J. MARTELL, Stuart MACGOWAN, Jake E. MCGREIG, Saqib MIR, Abhik MUKHOPADHYAY, Luca PARCA, Typhaine PAYSAN-LAFOSSE, Leandro RADUSKY, Antonio RIBEIRO, Luis SERRANO, Ian SILLITOE, Gulzar SINGH, Petr SKODA, Radka SVOBODOVÁ, Jonathan TYZACK, Alfonso VALENCIA, Eloy Villasclaras FERNANDEZ, Wim VRANKEN, Mark WASS, Janet THORNTON, Michael STERNBERG, Christine ORENGO and Sameer VELANKAR. PDBe-KB: a community-driven resource for structural and functional annotations. Nucleic acids research. Oxford: Oxford University Press, 2020, vol. 48, D1, p. "D344"-"D353", 10 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkz853.

@article{1730679,
   author = {Varadi, Mihaly and Bcrrisford, John and Deshpande, Mandar and Nair, Sreenath S. and Gutmanas, Aleksandras and Armstrong, David and Pravda, Lukáš and AlandLazikani, Bissan and Anyango, Stephen and Barton, Geoffrey J. and Berka, Karel and Blundell, Tom and Borkakoti, Neera and Dana, Jose and Das, Sayoni and Dey, Sucharita and Di Micco, Patrizio and Fraternali, Franca and Gibson, Toby and HelmerandCitterich, Manuela and Hoksza, David and Huang, LiangandChin and Jain, Rishabh and Jubb, Harry and Kannas, Christos and Kannan, Natarajan and Koča, Jaroslav and Krivak, Radoslav and Kumar, Manjeet and Levy, Emanuel D. and Madeira, F. and Madhusudhan, M. S. and Martell, Henry J. and MacGowan, Stuart and McGreig, Jake E. and Mir, Saqib and Mukhopadhyay, Abhik and Parca, Luca and PaysanandLafosse, Typhaine and Radusky, Leandro and Ribeiro, Antonio and Serrano, Luis and Sillitoe, Ian and Singh, Gulzar and Skoda, Petr and Svobodová, Radka and Tyzack, Jonathan and Valencia, Alfonso and Fernandez, Eloy Villasclaras and Vranken, Wim and Wass, Mark and Thornton, Janet and Sternberg, Michael and Orengo, Christine and Velankar, Sameer},
   article_location = {Oxford},
   article_number = {D1},
   doi = {http://dx.doi.org/10.1093/nar/gkz853},
   keywords = {PDBe-KB},
   language = {eng},
   issn = {0305-1048},
   journal = {Nucleic acids research},
   title = {PDBe-KB: a community-driven resource for structural and functional annotations},
   url = {https://doi.org/10.1093/nar/gkz853},
   volume = {48},
   year = {2020}
}

TY  - JOUR
ID  - 1730679
AU  - Varadi, Mihaly - Bcrrisford, John - Deshpande, Mandar - Nair, Sreenath S. - Gutmanas, Aleksandras - Armstrong, David - Pravda, Lukáš - Al-Lazikani, Bissan - Anyango, Stephen - Barton, Geoffrey J. - Berka, Karel - Blundell, Tom - Borkakoti, Neera - Dana, Jose - Das, Sayoni - Dey, Sucharita - Di Micco, Patrizio - Fraternali, Franca - Gibson, Toby - Helmer-Citterich, Manuela - Hoksza, David - Huang, Liang-Chin - Jain, Rishabh - Jubb, Harry - Kannas, Christos - Kannan, Natarajan - Koča, Jaroslav - Krivak, Radoslav - Kumar, Manjeet - Levy, Emanuel D. - Madeira, F. - Madhusudhan, M. S. - Martell, Henry J. - MacGowan, Stuart - McGreig, Jake E. - Mir, Saqib - Mukhopadhyay, Abhik - Parca, Luca - Paysan-Lafosse, Typhaine - Radusky, Leandro - Ribeiro, Antonio - Serrano, Luis - Sillitoe, Ian - Singh, Gulzar - Skoda, Petr - Svobodová, Radka - Tyzack, Jonathan - Valencia, Alfonso - Fernandez, Eloy Villasclaras - Vranken, Wim - Wass, Mark - Thornton, Janet - Sternberg, Michael - Orengo, Christine - Velankar, Sameer
PY  - 2020
TI  - PDBe-KB: a community-driven resource for structural and functional annotations
JF  - Nucleic acids research
VL  - 48
IS  - D1
SP  - "D344"-"D353"
EP  - "D344"-"D353"
PB  - Oxford University Press
SN  - 03051048
KW  - PDBe-KB
UR  - https://doi.org/10.1093/nar/gkz853
L2  - https://doi.org/10.1093/nar/gkz853
N2  - The Protein Data Bank in Europe-Knowledge Base (PDBe-KB, https://pdbe-kb.org) is a community-driven, collaborative resource for literature-derived, manually curated and computationally predicted structural and functional annotations of macro-molecular structure data, contained in the Protein Data Bank (PDB). The goal of PDBe-KB is two-fold: (i) to increase the visibility and reduce the fragmentation of annotations contributed by specialist data resources, and to make these data more findable, accessible, interoperable and reusable (FAIR) and (ii) to place macromolecular structure data in their biological context, thus facilitating their use by the broader scientific community in fundamental and applied research. Here, we describe the guidelines of this collaborative effort, the current status of contributed data, and the PDBe-KB infrastructure, which includes the data exchange format, the deposition system for added value annotations, the distributable database containing the assembled data, and programmatic access endpoints. We also describe a series of novel web-pages-the PDBe-KB aggregated views of structure data-which combine information on macromolecular structures from many PDB entries. We have recently released the first set of pages in this series, which provide an overview of available structural and functional information for a protein of interest, referenced by a UniProtKB accession.
ER  -

VARADI, Mihaly, John BCRRISFORD, Mandar DESHPANDE, Sreenath S. NAIR, Aleksandras GUTMANAS, David ARMSTRONG, Lukáš PRAVDA, Bissan AL-LAZIKANI, Stephen ANYANGO, Geoffrey J. BARTON, Karel BERKA, Tom BLUNDELL, Neera BORKAKOTI, Jose DANA, Sayoni DAS, Sucharita DEY, Patrizio DI MICCO, Franca FRATERNALI, Toby GIBSON, Manuela HELMER-CITTERICH, David HOKSZA, Liang-Chin HUANG, Rishabh JAIN, Harry JUBB, Christos KANNAS, Natarajan KANNAN, Jaroslav KOČA, Radoslav KRIVAK, Manjeet KUMAR, Emanuel D. LEVY, F. MADEIRA, M. S. MADHUSUDHAN, Henry J. MARTELL, Stuart MACGOWAN, Jake E. MCGREIG, Saqib MIR, Abhik MUKHOPADHYAY, Luca PARCA, Typhaine PAYSAN-LAFOSSE, Leandro RADUSKY, Antonio RIBEIRO, Luis SERRANO, Ian SILLITOE, Gulzar SINGH, Petr SKODA, Radka SVOBODOVÁ, Jonathan TYZACK, Alfonso VALENCIA, Eloy Villasclaras FERNANDEZ, Wim VRANKEN, Mark WASS, Janet THORNTON, Michael STERNBERG, Christine ORENGO and Sameer VELANKAR. PDBe-KB: a community-driven resource for structural and functional annotations. \textit{Nucleic acids research}. Oxford: Oxford University Press, 2020, vol.~48, D1, p.~''D344''-''D353'', 10 pp. ISSN~0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkz853.

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