PDBe-KB: collaboratively defining the biological context of structural data
Autoři
VARADI, Mihaly; Stephen ANYANGO; David ARMSTRONG; John BERRISFORD; Preeti CHOUDHARY; Mandar DESHPANDE; Nurul NADZIRIN; Sreenatha S. NAIR; Lukas PRAVDA; Ahsan TANWEER; Bissan AL-LAZIKANI; Claudia ANDREINI; Geoffrey J. BARTON; David BEDNÁŘ (203 Česká republika, domácí); Karel BERKA; Tom BLUNDELL; Kelly P. BROCK; Jose MARIA CARAZO; Jiří DAMBORSKÝ (203 Česká republika, garant, domácí); Alessia DAVID; Sucharita DEY; Roland DUNBRACK; Fernandez Juan RECIO; Franca FRATERNALI; Toby GIBSON; Manuela HELMER-CITTERICH; David HOKSZA; Thomas HOPF; David JAKUBEC; Natarajan KANNAN; Radoslav KRIVAK; Manjeet KUMAR; Emmanuel D. LEVY; Nir LONDON; Jose Ramon MACIAS; Madhusudhan M. SRIVATSAN; Debora S. MARKS; Lennart MARTENS; Stuart A. MCGOWAN; Jake E. MCGREIG; Vivek MODI; Gonzalo R. PARRA; Gerardo PEPE; Damiano PIOVESAN; Jaime PRILUSKY; Valeria PUTIGNANO; Leandro G. RADUSKY; Pathmanaban RAMASAMY; Atilio O. RAUSCH; Nathalie REUTER; Luis A. RODRIGUEZ; Nathan J. ROLLINS; Antonio ROSATO; Luis SERRANO; Gulzar SINGH; Petr SKODA; Carlos Oscar S. SORZANO; Jan ŠTOURAČ (203 Česká republika, domácí); Joanna I. SULKOWSKA; Radka SVOBODOVÁ (203 Česká republika, domácí); Natalia TICHSHENKO; Silvio C. E. TOSATTO; Wim VRANKEN; Mark N. WASS; Dandan XUE; Daniel ZAIDMAN; Janet THORNTON; Michael STERNBERG; Christine ORENGO a Sameer VELANKAR
Vydání
Nucleic acids research, Oxford, Oxford University Press, 2022, 0305-1048
The Protein Data Bank in Europe - Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological context by developing standardised data exchange formats and integrating functional annotations from the contributing partner resources into a knowledge graph that can provide valuable biological insights. Since we described PDBe-KB in 2019, there have been significant improvements in the variety of available annotation data sets and user functionality. Here, we provide an overview of the consortium, highlighting the addition of annotations such as predicted covalent binders, phosphorylation sites, effects of mutations on the protein structure and energetic local frustration. In addition, we describe a library of reusable web-based visualisation components and introduce new features such as a bulk download data service and a novel superposition service that generates clusters of superposed protein chains weekly for the whole PDB archive.
Návaznosti
823839, interní kód MU
Název: European Proteomics Infrastructure Consortium providing Access (Akronym: EPIC-XS)
Investor: Evropská unie, European Proteomics Infrastructure Consortium providing Access, RI Research Infrastructures (Excellent Science)
VARADI, Mihaly; Stephen ANYANGO; David ARMSTRONG; John BERRISFORD; Preeti CHOUDHARY; Mandar DESHPANDE; Nurul NADZIRIN; Sreenatha S. NAIR; Lukas PRAVDA; Ahsan TANWEER; Bissan AL-LAZIKANI; Claudia ANDREINI; Geoffrey J. BARTON; David BEDNÁŘ; Karel BERKA; Tom BLUNDELL; Kelly P. BROCK; Jose MARIA CARAZO; Jiří DAMBORSKÝ; Alessia DAVID; Sucharita DEY; Roland DUNBRACK; Fernandez Juan RECIO; Franca FRATERNALI; Toby GIBSON; Manuela HELMER-CITTERICH; David HOKSZA; Thomas HOPF; David JAKUBEC; Natarajan KANNAN; Radoslav KRIVAK; Manjeet KUMAR; Emmanuel D. LEVY; Nir LONDON; Jose Ramon MACIAS; Madhusudhan M. SRIVATSAN; Debora S. MARKS; Lennart MARTENS; Stuart A. MCGOWAN; Jake E. MCGREIG; Vivek MODI; Gonzalo R. PARRA; Gerardo PEPE; Damiano PIOVESAN; Jaime PRILUSKY; Valeria PUTIGNANO; Leandro G. RADUSKY; Pathmanaban RAMASAMY; Atilio O. RAUSCH; Nathalie REUTER; Luis A. RODRIGUEZ; Nathan J. ROLLINS; Antonio ROSATO; Luis SERRANO; Gulzar SINGH; Petr SKODA; Carlos Oscar S. SORZANO; Jan ŠTOURAČ; Joanna I. SULKOWSKA; Radka SVOBODOVÁ; Natalia TICHSHENKO; Silvio C. E. TOSATTO; Wim VRANKEN; Mark N. WASS; Dandan XUE; Daniel ZAIDMAN; Janet THORNTON; Michael STERNBERG; Christine ORENGO a Sameer VELANKAR. PDBe-KB: collaboratively defining the biological context of structural data. Nucleic acids research. Oxford: Oxford University Press, 2022, roč. 50, D1, s. "D534"-"D542", 9 s. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkab988.
@article{1860103, author = {Varadi, Mihaly and Anyango, Stephen and Armstrong, David and Berrisford, John and Choudhary, Preeti and Deshpande, Mandar and Nadzirin, Nurul and Nair, Sreenatha S. and Pravda, Lukas and Tanweer, Ahsan and AlandLazikani, Bissan and Andreini, Claudia and Barton, Geoffrey J. and Bednář, David and Berka, Karel and Blundell, Tom and Brock, Kelly P. and Maria Carazo, Jose and Damborský, Jiří and David, Alessia and Dey, Sucharita and Dunbrack, Roland and Recio, Fernandez Juan and Fraternali, Franca and Gibson, Toby and HelmerandCitterich, Manuela and Hoksza, David and Hopf, Thomas and Jakubec, David and Kannan, Natarajan and Krivak, Radoslav and Kumar, Manjeet and Levy, Emmanuel D. and London, Nir and Macias, Jose Ramon and Srivatsan, Madhusudhan M. and Marks, Debora S. and Martens, Lennart and McGowan, Stuart A. and McGreig, Jake E. and Modi, Vivek and Parra, Gonzalo R. and Pepe, Gerardo and Piovesan, Damiano and Prilusky, Jaime and Putignano, Valeria and Radusky, Leandro G. and Ramasamy, Pathmanaban and Rausch, Atilio O. and Reuter, Nathalie and Rodriguez, Luis A. and Rollins, Nathan J. and Rosato, Antonio and Serrano, Luis and Singh, Gulzar and Skoda, Petr and Sorzano, Carlos Oscar S. and Štourač, Jan and Sulkowska, Joanna I. and Svobodová, Radka and Tichshenko, Natalia and Tosatto, Silvio C. E. and Vranken, Wim and Wass, Mark N. and Xue, Dandan and Zaidman, Daniel 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/gkab988}, keywords = {WEB SERVER; PROTEIN; PREDICT}, language = {eng}, issn = {0305-1048}, journal = {Nucleic acids research}, title = {PDBe-KB: collaboratively defining the biological context of structural data}, url = {https://academic.oup.com/nar/article/50/D1/D534/6424755?login=true}, volume = {50}, year = {2022} }
TY - JOUR ID - 1860103 AU - Varadi, Mihaly - Anyango, Stephen - Armstrong, David - Berrisford, John - Choudhary, Preeti - Deshpande, Mandar - Nadzirin, Nurul - Nair, Sreenatha S. - Pravda, Lukas - Tanweer, Ahsan - Al-Lazikani, Bissan - Andreini, Claudia - Barton, Geoffrey J. - Bednář, David - Berka, Karel - Blundell, Tom - Brock, Kelly P. - Maria Carazo, Jose - Damborský, Jiří - David, Alessia - Dey, Sucharita - Dunbrack, Roland - Recio, Fernandez Juan - Fraternali, Franca - Gibson, Toby - Helmer-Citterich, Manuela - Hoksza, David - Hopf, Thomas - Jakubec, David - Kannan, Natarajan - Krivak, Radoslav - Kumar, Manjeet - Levy, Emmanuel D. - London, Nir - Macias, Jose Ramon - Srivatsan, Madhusudhan M. - Marks, Debora S. - Martens, Lennart - McGowan, Stuart A. - McGreig, Jake E. - Modi, Vivek - Parra, Gonzalo R. - Pepe, Gerardo - Piovesan, Damiano - Prilusky, Jaime - Putignano, Valeria - Radusky, Leandro G. - Ramasamy, Pathmanaban - Rausch, Atilio O. - Reuter, Nathalie - Rodriguez, Luis A. - Rollins, Nathan J. - Rosato, Antonio - Serrano, Luis - Singh, Gulzar - Skoda, Petr - Sorzano, Carlos Oscar S. - Štourač, Jan - Sulkowska, Joanna I. - Svobodová, Radka - Tichshenko, Natalia - Tosatto, Silvio C. E. - Vranken, Wim - Wass, Mark N. - Xue, Dandan - Zaidman, Daniel - Thornton, Janet - Sternberg, Michael - Orengo, Christine - Velankar, Sameer PY - 2022 TI - PDBe-KB: collaboratively defining the biological context of structural data JF - Nucleic acids research VL - 50 IS - D1 SP - "D534"-"D542" EP - "D534"-"D542" PB - Oxford University Press SN - 03051048 KW - WEB SERVER KW - PROTEIN KW - PREDICT UR - https://academic.oup.com/nar/article/50/D1/D534/6424755?login=true N2 - The Protein Data Bank in Europe - Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological context by developing standardised data exchange formats and integrating functional annotations from the contributing partner resources into a knowledge graph that can provide valuable biological insights. Since we described PDBe-KB in 2019, there have been significant improvements in the variety of available annotation data sets and user functionality. Here, we provide an overview of the consortium, highlighting the addition of annotations such as predicted covalent binders, phosphorylation sites, effects of mutations on the protein structure and energetic local frustration. In addition, we describe a library of reusable web-based visualisation components and introduce new features such as a bulk download data service and a novel superposition service that generates clusters of superposed protein chains weekly for the whole PDB archive. ER -
VARADI, Mihaly; Stephen ANYANGO; David ARMSTRONG; John BERRISFORD; Preeti CHOUDHARY; Mandar DESHPANDE; Nurul NADZIRIN; Sreenatha S. NAIR; Lukas PRAVDA; Ahsan TANWEER; Bissan AL-LAZIKANI; Claudia ANDREINI; Geoffrey J. BARTON; David BEDNÁŘ; Karel BERKA; Tom BLUNDELL; Kelly P. BROCK; Jose MARIA CARAZO; Jiří DAMBORSKÝ; Alessia DAVID; Sucharita DEY; Roland DUNBRACK; Fernandez Juan RECIO; Franca FRATERNALI; Toby GIBSON; Manuela HELMER-CITTERICH; David HOKSZA; Thomas HOPF; David JAKUBEC; Natarajan KANNAN; Radoslav KRIVAK; Manjeet KUMAR; Emmanuel D. LEVY; Nir LONDON; Jose Ramon MACIAS; Madhusudhan M. SRIVATSAN; Debora S. MARKS; Lennart MARTENS; Stuart A. MCGOWAN; Jake E. MCGREIG; Vivek MODI; Gonzalo R. PARRA; Gerardo PEPE; Damiano PIOVESAN; Jaime PRILUSKY; Valeria PUTIGNANO; Leandro G. RADUSKY; Pathmanaban RAMASAMY; Atilio O. RAUSCH; Nathalie REUTER; Luis A. RODRIGUEZ; Nathan J. ROLLINS; Antonio ROSATO; Luis SERRANO; Gulzar SINGH; Petr SKODA; Carlos Oscar S. SORZANO; Jan ŠTOURAČ; Joanna I. SULKOWSKA; Radka SVOBODOVÁ; Natalia TICHSHENKO; Silvio C. E. TOSATTO; Wim VRANKEN; Mark N. WASS; Dandan XUE; Daniel ZAIDMAN; Janet THORNTON; Michael STERNBERG; Christine ORENGO a Sameer VELANKAR. PDBe-KB: collaboratively defining the biological context of structural data. \textit{Nucleic acids research}. Oxford: Oxford University Press, 2022, roč.~50, D1, s.~''D534''-''D542'', 9 s. ISSN~0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkab988.
