PDBE-KB: A community-driven resource for structural and functional annotations

Mihaly Varadi; John Berrisford; Mandar Deshpande; Sreenath S. Nair; Aleksandras Gutmanas; David Armstrong; Lukas 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 Koca; Radoslav Krivak; Manjeet Kumar; Emmanuel 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 Svobodova; Jonathan Tyzack; Alfonso Valencia; Eloy Villasclaras Fernandez; Wim Vranken; Mark Wass; Janet Thornton; Michael Sternberg; Christine Orengo; Sameer Velankar

doi:10.1093/nar/gkz853

PDBE-KB: A community-driven resource for structural and functional annotations

Mihaly Varadi, John Berrisford, Mandar Deshpande, Sreenath S. Nair, Aleksandras Gutmanas, David Armstrong, Lukas 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-CitterichDavid Hoksza, Liang Chin Huang, Rishabh Jain, Harry Jubb, Christos Kannas, Natarajan Kannan, Jaroslav Koca, Radoslav Krivak, Manjeet Kumar, Emmanuel 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 Svobodova, Jonathan Tyzack, Alfonso Valencia, Eloy Villasclaras Fernandez, Wim Vranken, Mark Wass, Janet Thornton, Michael Sternberg, Christine Orengo, Sameer Velankar

Research output: Contribution to journal › Article › peer-review

68 Scopus citations

Abstract

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 macromolecular 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.

Original language	English (US)
Pages (from-to)	D344-D353
Journal	Nucleic acids research
Volume	48
DOIs	https://doi.org/10.1093/nar/gkz853
State	Published - 2020
Externally published	Yes

ASJC Scopus subject areas

Genetics

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10.1093/nar/gkz853

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Varadi, M., Berrisford, J., Deshpande, M., Nair, S. S., Gutmanas, A., Armstrong, D., Pravda, L., Al-Lazikani, B., Anyango, S., Barton, G. J., Berka, K., Blundell, T., Borkakoti, N., Dana, J., Das, S., Dey, S., Di Micco, P., Fraternali, F., Gibson, T., ... Velankar, S. (2020). PDBE-KB: A community-driven resource for structural and functional annotations. Nucleic acids research, 48, D344-D353. https://doi.org/10.1093/nar/gkz853

Varadi, M, Berrisford, J, Deshpande, M, Nair, SS, Gutmanas, A, Armstrong, D, Pravda, L, Al-Lazikani, B, Anyango, S, Barton, GJ, Berka, K, Blundell, T, Borkakoti, N, Dana, J, Das, S, Dey, S, Di Micco, P, Fraternali, F, Gibson, T, Helmer-Citterich, M, Hoksza, D, Huang, LC, Jain, R, Jubb, H, Kannas, C, Kannan, N, Koca, J, Krivak, R, Kumar, M, Levy, ED, Madeira, F, Madhusudhan, MS, Martell, HJ, MacGowan, S, McGreig, JE, Mir, S, Mukhopadhyay, A, Parca, L, Paysan-Lafosse, T, Radusky, L, Ribeiro, A, Serrano, L, Sillitoe, I, Singh, G, Skoda, P, Svobodova, R, Tyzack, J, Valencia, A, Fernandez, EV, Vranken, W, Wass, M, Thornton, J, Sternberg, M, Orengo, C & Velankar, S 2020, 'PDBE-KB: A community-driven resource for structural and functional annotations', Nucleic acids research, vol. 48, pp. D344-D353. https://doi.org/10.1093/nar/gkz853

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title = "PDBE-KB: A community-driven resource for structural and functional annotations",

abstract = "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 macromolecular 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.",

author = "Mihaly Varadi and John Berrisford and Mandar Deshpande and Nair, {Sreenath S.} and Aleksandras Gutmanas and David Armstrong and Lukas Pravda and Bissan Al-Lazikani and Stephen Anyango and Barton, {Geoffrey J.} and Karel Berka and Tom Blundell and Neera Borkakoti and Jose Dana and Sayoni Das and Sucharita Dey and {Di Micco}, Patrizio and Franca Fraternali and Toby Gibson and Manuela Helmer-Citterich and David Hoksza and Huang, {Liang Chin} and Rishabh Jain and Harry Jubb and Christos Kannas and Natarajan Kannan and Jaroslav Koca and Radoslav Krivak and Manjeet Kumar and Levy, {Emmanuel D.} and F. Madeira and Madhusudhan, {M. S.} and Martell, {Henry J.} and Stuart MacGowan and McGreig, {Jake E.} and Saqib Mir and Abhik Mukhopadhyay and Luca Parca and Typhaine Paysan-Lafosse and Leandro Radusky and Antonio Ribeiro and Luis Serrano and Ian Sillitoe and Gulzar Singh and Petr Skoda and Radka Svobodova and Jonathan Tyzack and Alfonso Valencia and Fernandez, {Eloy Villasclaras} and Wim Vranken and Mark Wass and Janet Thornton and Michael Sternberg and Christine Orengo and Sameer Velankar",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2019.",

year = "2020",

doi = "10.1093/nar/gkz853",

language = "English (US)",

volume = "48",

pages = "D344--D353",

journal = "Nucleic acids research",

issn = "0305-1048",

publisher = "Oxford University Press",

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T2 - A community-driven resource for structural and functional annotations

AU - Varadi, Mihaly

AU - Berrisford, John

AU - Deshpande, Mandar

AU - Nair, Sreenath S.

AU - Gutmanas, Aleksandras

AU - Armstrong, David

AU - Pravda, Lukas

AU - Al-Lazikani, Bissan

AU - Anyango, Stephen

AU - Barton, Geoffrey J.

AU - Berka, Karel

AU - Blundell, Tom

AU - Borkakoti, Neera

AU - Dana, Jose

AU - Das, Sayoni

AU - Dey, Sucharita

AU - Di Micco, Patrizio

AU - Fraternali, Franca

AU - Gibson, Toby

AU - Helmer-Citterich, Manuela

AU - Hoksza, David

AU - Huang, Liang Chin

AU - Jain, Rishabh

AU - Jubb, Harry

AU - Kannas, Christos

AU - Kannan, Natarajan

AU - Koca, Jaroslav

AU - Krivak, Radoslav

AU - Kumar, Manjeet

AU - Levy, Emmanuel D.

AU - Madeira, F.

AU - Madhusudhan, M. S.

AU - Martell, Henry J.

AU - MacGowan, Stuart

AU - McGreig, Jake E.

AU - Mir, Saqib

AU - Mukhopadhyay, Abhik

AU - Parca, Luca

AU - Paysan-Lafosse, Typhaine

AU - Radusky, Leandro

AU - Ribeiro, Antonio

AU - Serrano, Luis

AU - Sillitoe, Ian

AU - Singh, Gulzar

AU - Skoda, Petr

AU - Svobodova, Radka

AU - Tyzack, Jonathan

AU - Valencia, Alfonso

AU - Fernandez, Eloy Villasclaras

AU - Vranken, Wim

AU - Wass, Mark

AU - Thornton, Janet

AU - Sternberg, Michael

AU - Orengo, Christine

AU - Velankar, Sameer

PY - 2020

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DO - 10.1093/nar/gkz853

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ER -

PDBE-KB: A community-driven resource for structural and functional annotations

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