John M. Berrisford

According to our database, John M. Berrisford authored at least 11 papers between 2014 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank.

Preeti Choudhary, Zukang Feng, John M. Berrisford, Henry Chao, Yasuyo Ikegawa, Ezra Peisach, Dennis W. Piehl, James Smith, Ahsan Tanweer, Mihaly Varadi, John D. Westbrook, Jasmine Young, Ardan Patwardhan, Kyle L. Morris, Jeffrey C. Hoch, Genji Kurisu, Sameer Velankar, Stephen K. Burley

Database J. Biol. Databases Curation, January, 2024

2022

PDBe-KB: collaboratively defining the biological context of structural data.

Mihaly Varadi, Stephen Anyango, David R. Armstrong, John M. Berrisford, Preeti Choudhary, Mandar S. Deshpande, Nurul Nadzirin, Sreenath Nair, Lukás Pravda, Ahsan Tanweer, Bissan Al-Lazikani, Claudia Andreini, Geoffrey J. Barton, David Bednar, Karel Berka, Tom L. Blundell, Kelly Brock, José María Carazo, Jirí Damborský, Alessia David, Sucharita Dey, Roland L. Dunbrack Jr., Juan Fernández-Recio, Franca Fraternali, Toby J. Gibson, Manuela Helmer-Citterich, David Hoksza, Thomas A. Hopf, David Jakubec, Natarajan Kannan, Radoslav Krivák, Manjeet Kumar, Emmanuel D. Levy, Nir London, José Ramón Macías, Mallur Srivatsan Madhusudhan, Debora S. Marks, Lennart Martens, Stuart A McGowan, Jake E. McGreig, Vivek Modi, R. Gonzalo 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, Pawel Rubach, Luis Serrano, Gulzar Singh, Petr Skoda, Carlos Oscar Sánchez Sorzano, Jan Stourac, Joanna I. Sulkowska, Radka Svobodová Vareková, Natalia Tichshenko, Silvio C. E. Tosatto, Wim F. Vranken, Mark N. Wass, Dandan Xue, Daniel Zaidman, Janet M. Thornton, Michael J. E. Sternberg, Christine A. Orengo, Sameer Velankar

Nucleic Acids Res., 2022

2021

PDBe aggregated API: programmatic access to an integrative knowledge graph of molecular structure data.

Sreenath Nair, Mihaly Varadi, Nurul Nadzirin, Lukás Pravda, Stephen Anyango, Saqib Mir, John M. Berrisford, David R. Armstrong, Aleksandras Gutmanas, Sameer Velankar

Bioinform., 2021

2020

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

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

Nucleic Acids Res., 2020

PDBe: improved findability of macromolecular structure data in the PDB.

David R. Armstrong, John M. Berrisford, Matthew J. Conroy, Aleksandras Gutmanas, Stephen Anyango, Preeti Choudhary, Alice R. Clark, Jose M. Dana, Mandar S. Deshpande, Roisin Dunlop, Paul J. Gane, Romana Gáborová, Deepti Gupta, Pauline Haslam, Jaroslav Koca, Lora Mak, Saqib Mir, Abhik Mukhopadhyay, Nurul Nadzirin, Sreenath Nair, Typhaine Paysan-Lafosse, Lukás Pravda, David Sehnal, Osman Salih, Oliver S. Smart, James Tolchard, Mihaly Varadi, Radka Svobodová Vareková, Hossam Zaki, Gerard J. Kleywegt, Sameer Velankar

Nucleic Acids Res., 2020

2019

Protein Structure Databases.

David R. Armstrong, John M. Berrisford, Matthew J. Conroy, Alice R. Clark, Deepti Gupta, Abhik Mukhopadhyay

Proceedings of the Encyclopedia of Bioinformatics and Computational Biology - Volume 2, 2019

2018

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe.

Saqib Mir, Younes Alhroub, Stephen Anyango, David R. Armstrong, John M. Berrisford, Alice R. Clark, Matthew J. Conroy, Jose M. Dana, Mandar S. Deshpande, Deepti Gupta, Aleksandras Gutmanas, Pauline Haslam, Lora Mak, Abhik Mukhopadhyay, Nurul Nadzirin, Typhaine Paysan-Lafosse, David Sehnal, Sanchayita Sen, Oliver S. Smart, Mihaly Varadi, Gerard J. Kleywegt, Sameer Velankar

Nucleic Acids Res., 2018

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.

Jasmine Young, John D. Westbrook, Zukang Feng, Ezra Peisach, Irina Persikova, Raul Sala, Sanchayita Sen, John M. Berrisford, Jawahar Swaminathan, Thomas J. Oldfield, Aleksandras Gutmanas, Reiko Igarashi, David R. Armstrong, Kumaran Baskaran, Li Chen, Minyu Chen, Alice R. Clark, Luigi Di Costanzo, Dimitris Dimitropoulos, Guanghua Gao, Sutapa Ghosh, Swanand P. Gore, Vladimir Guranovic, Pieter M. S. Hendrickx, Brian P. Hudson, Yasuyo Ikegawa, Yumiko Kengaku, Catherine L. Lawson, Yuhe Liang, Lora Mak, Abhik Mukhopadhyay, Buvaneswari Coimbatore Narayanan, Kayoko Nishiyama, Ardan Patwardhan, Gaurav Sahni, Eduardo Sanz-García, Junko Sato, Monica Sekharan, Chenghua Shao, Oliver S. Smart, Lihua Tan, Glen van Ginkel, Huanwang Yang, Marina Zhuravleva, John L. Markley, Haruki Nakamura, Genji Kurisu, Gerard J. Kleywegt, Sameer Velankar, Helen M. Berman, Stephen K. Burley

Database J. Biol. Databases Curation, 2018

2016

PDBe: improved accessibility of macromolecular structure data from PDB and EMDB.

Sameer Velankar, Glen van Ginkel, Younes Alhroub, Gary M. Battle, John M. Berrisford, Matthew J. Conroy, Jose M. Dana, Swanand P. Gore, Aleksandras Gutmanas, Pauline Haslam, Pieter M. S. Hendrickx, Ingvar C. Lagerstedt, Saqib Mir, Manuel A. Fernandez Montecelo, Abhik Mukhopadhyay, Thomas J. Oldfield, Ardan Patwardhan, Eduardo Sanz-García, Sanchayita Sen, Robert A. Slowley, Michael E. Wainwright, Mandar S. Deshpande, Andrii Iudin, Gaurav Sahni, José Salavert Torres, Miriam Hirshberg, Lora Mak, Nurul Nadzirin, David R. Armstrong, Alice R. Clark, Oliver S. Smart, Paul K. Korir, Gerard J. Kleywegt

Nucleic Acids Res., 2016

2014

PDBe: Protein Data Bank in Europe.

Aleksandras Gutmanas, Younes Alhroub, Gary M. Battle, John M. Berrisford, Estelle Bochet, Matthew J. Conroy, Jose M. Dana, Manuel A. Fernandez Montecelo, Glen van Ginkel, Swanand P. Gore, Pauline Haslam, Rowan Hatherley, Pieter M. S. Hendrickx, Miriam Hirshberg, Ingvar C. Lagerstedt, Saqib Mir, Abhik Mukhopadhyay, Thomas J. Oldfield, Ardan Patwardhan, Luana Rinaldi, Gaurav Sahni, Eduardo Sanz-García, Sanchayita Sen, Robert A. Slowley, Sameer Velankar, Michael E. Wainwright, Gerard J. Kleywegt

Nucleic Acids Res., 2014

Small molecule annotation for the Protein Data Bank.

Sanchayita Sen, Jasmine Young, John M. Berrisford, Minyu Chen, Matthew J. Conroy, Shuchismita Dutta, Luigi Di Costanzo, Guanghua Gao, Sutapa Ghosh, Brian P. Hudson, Reiko Igarashi, Yumiko Kengaku, Yuhe Liang, Ezra Peisach, Irina Persikova, Abhik Mukhopadhyay, Buvaneswari Coimbatore Narayanan, Gaurav Sahni, Junko Sato, Monica Sekharan, Chenghua Shao, Lihua Tan, Marina Zhuravleva

Database J. Biol. Databases Curation, 2014