Sameer Velankar

Publication Activity (10 Years)

Years Active: 2008-2024
Publications (10 Years): 25

Top Topics

Protein Structure

Top Venues

Nucleic Acids Res.

Briefings Bioinform.

Database J. Biol. Databases Curation

Publications

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
PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank. Database J. Biol. Databases Curation 2024 (2024)
Matthew Thakur, Alex Bateman, Cath Brooksbank, Mallory Ann Freeberg, Melissa Harrison, Matthew Hartley, Thomas M. Keane, Gerard J. Kleywegt, Andrew Leach, Maria Levchenko, Sarah L. Morgan, Ellen M. McDonagh, Sandra E. Orchard, Irene Papatheodorou, Sameer Velankar, Juan Antonio Vizcaíno, Rick Witham, Barbara Zdrazil, Johanna R. McEntyre
EMBL's European Bioinformatics Institute (EMBL-EBI) in 2022. Nucleic Acids Res. 51 (D1) (2023)
Ibrahim Roshan Kunnakkattu, Preeti Choudhary, Lukás Pravda, Nurul Nadzirin, Oliver S. Smart, Qi Yuan, Stephen Anyango, Sreenath Nair, Mihaly Varadi, Sameer Velankar
PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank. J. Cheminformatics 15 (1) (2023)
Adam Midlik, Sreenath Nair, Stephen Anyango, Mandar S. Deshpande, David Sehnal, Mihaly Varadi, Sameer Velankar
PDBImages: a command-line tool for automated macromolecular structure visualization. Bioinform. 39 (12) (2023)
Mihaly Varadi, Stephen Anyango, Mandar S. Deshpande, Sreenath Nair, Cindy Natassia, Galabina Yordanova, David Yuan, Oana Stroe, Gemma Wood, Agata Laydon, Augustin Zídek, Tim Green, Kathryn Tunyasuvunakool, Stig Petersen, John Jumper, Ellen Clancy, Richard Green, Ankur Vora, Mira Lutfi, Michael Figurnov, Andrew Cowie, Nicole Hobbs, Pushmeet Kohli, Gerard J. Kleywegt, Ewan Birney, Demis Hassabis, Sameer Velankar
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Res. 50 (D1) (2022)
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
PDBe-KB: collaboratively defining the biological context of structural data. Nucleic Acids Res. 50 (D1) (2022)
Neeladri Sen, Ivan Anishchenko, Nicola Bordin, Ian Sillitoe, Sameer Velankar, David Baker, Christine A. Orengo
Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs. Briefings Bioinform. 23 (4) (2022)
David Sehnal, Sebastian Bittrich, Mandar S. Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K. Burley, Jaroslav Koca, Alexander S. Rose
Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. Nucleic Acids Res. 49 (Webserver-Issue) (2021)
Sreenath Nair, Mihaly Varadi, Nurul Nadzirin, Lukás Pravda, Stephen Anyango, Saqib Mir, John M. Berrisford, David R. Armstrong, Aleksandras Gutmanas, Sameer Velankar
PDBe aggregated API: programmatic access to an integrative knowledge graph of molecular structure data. Bioinform. 37 (21) (2021)
Glen van Ginkel, Lukás Pravda, Jose M. Dana, Mihaly Varadi, Peter A. Keller, Stephen Anyango, Sameer Velankar
PDBeCIF: an open-source mmCIF/CIF parsing and processing package. BMC Bioinform. 22 (1) (2021)
Vaishali P. Waman, Neeladri Sen, Mihaly Varadi, Antoine Daina, Shoshana J. Wodak, Vincent Zoete, Sameer Velankar, Christine A. Orengo
The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies. Briefings Bioinform. 22 (2) (2021)
Ian Sillitoe, Antonina Andreeva, Tom L. Blundell, Daniel W. A. Buchan, Robert D. Finn, Julian Gough, David T. Jones, Lawrence A. Kelley, Typhaine Paysan-Lafosse, Su Datt Lam, Alexey G. Murzin, Arun Prasad Pandurangan, Gustavo A. Salazar, Marcin J. Skwark, Michael J. E. Sternberg, Sameer Velankar, Christine A. Orengo
Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation. Nucleic Acids Res. 48 (Database-Issue) (2020)
David Sehnal, Sebastian Bittrich, Sameer Velankar, Jaroslav Koca, Radka Svobodová Vareková, Stephen K. Burley, Alexander S. Rose
BinaryCIF and CIFTools - Lightweight, efficient and extensible macromolecular data management. PLoS Comput. Biol. 16 (10) (2020)
Rachel Drysdale, Charles E. Cook, Robert Petryszak, Vivienne Baillie Gerritsen, Mary Barlow, Elisabeth Gasteiger, Franziska Gruhl, Jürgen Haas, Jerry Lanfear, Rodrigo Lopez, Nicole Redaschi, Heinz Stockinger, Daniel Teixeira, Aravind Venkatesan, Alex Bateman, Alan Bridge, Guy Cochrane, Robert D. Finn, Frank Oliver Glöckner, Marc Hanauer, Thomas M. Keane, Andrew Leach, Luana Licata, Per Oksvold, Sandra E. Orchard, Christine A. Orengo, Helen E. Parkinson, Bengt Persson, Pablo Porras, Jordi Rambla, Ana Rath, Charlotte Rodwell, Ugis Sarkans, Dietmar Schomburg, Ian Sillitoe, J. Dylan Spalding, Mathias Uhlén, Sameer Velankar, Juan Antonio Vizcaíno, Kalle von Feilitzen, Christian von Mering, Andrew D. Yates, Niklas Blomberg, Christine Durinx, Johanna R. McEntyre
The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences. Bioinform. 36 (8) (2020)
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
PDBe: improved findability of macromolecular structure data in the PDB. Nucleic Acids Res. 48 (Database-Issue) (2020)
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
PDBe-KB: a community-driven resource for structural and functional annotations. Nucleic Acids Res. 48 (Database-Issue) (2020)
Jose M. Dana, Aleksandras Gutmanas, Nidhi Tyagi, Guoying Qi, Claire O'Donovan, Maria Jesus Martin, Sameer Velankar
SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins. Nucleic Acids Res. 47 (Database-Issue) (2019)
Abhik Mukhopadhyay, Neera Borkakoti, Lukás Pravda, Jonathan D. Tyzack, Janet M. Thornton, Sameer Velankar
Finding enzyme cofactors in Protein Data Bank. Bioinform. 35 (18) (2019)
David Sehnal, Alexander S. Rose, Jaroslav Koca, Stephen K. Burley, Sameer Velankar
Mol*: Towards a Common Library and Tools for Web Molecular Graphics. MolVa@EuroVis (2018)
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
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. Database J. Biol. Databases Curation 2018 (2018)
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
PDBe: towards reusable data delivery infrastructure at protein data bank in Europe. Nucleic Acids Res. 46 (Database-Issue) (2018)
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
PDBe: improved accessibility of macromolecular structure data from PDB and EMDB. Nucleic Acids Res. 44 (Database-Issue) (2016)
Tony E. Lewis, Ian Sillitoe, Antonina Andreeva, Tom L. Blundell, Daniel W. A. Buchan, Cyrus Chothia, Domenico Cozzetto, Jose M. Dana, Ioannis Filippis, Julian Gough, David T. Jones, Lawrence A. Kelley, Gerard J. Kleywegt, Federico Minneci, Jaina Mistry, Alexey G. Murzin, Bernardo Ochoa-Montaño, Matt E. Oates, Marco Punta, Owen J. L. Rackham, Jonathan Stahlhacke, Michael J. E. Sternberg, Sameer Velankar, Christine A. Orengo
Genome3D: exploiting structure to help users understand their sequences. Nucleic Acids Res. 43 (Database-Issue) (2015)
Birgit H. M. Meldal, Oscar Forner-Martinez, Maria C. Costanzo, Jose M. Dana, Janos Demeter, Marine Dumousseau, Selina S. Dwight, Anna Gaulton, Luana Licata, Anna N. Melidoni, Sylvie Ricard-Blum, Bernd Roechert, Marek S. Skrzypek, Manu Tiwari, Sameer Velankar, Edith D. Wong, Henning Hermjakob, Sandra E. Orchard
The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43 (Database-Issue) (2015)
John D. Westbrook, Chenghua Shao, Zukang Feng, Marina Zhuravleva, Sameer Velankar, Jasmine Young
The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank. Bioinform. 31 (8) (2015)
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
PDBe: Protein Data Bank in Europe. Nucleic Acids Res. 42 (Database-Issue) (2014)
Sameer Velankar, Jose M. Dana, Julius O. B. Jacobsen, Glen van Ginkel, Paul J. Gane, Jie Luo, Thomas J. Oldfield, Claire O'Donovan, Maria Jesus Martin, Gerard J. Kleywegt
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. Nucleic Acids Res. 41 (Database-Issue) (2013)
Rafael Alcántara, Joseph Onwubiko, Hong Cao, Paula de Matos, Jennifer A. Cham, Julius O. B. Jacobsen, Gemma L. Holliday, Julia D. Fischer, Syed Asad Rahman, Bijay Jassal, Mickael Goujon, Francis Rowland, Sameer Velankar, Rodrigo Lopez, John P. Overington, Gerard J. Kleywegt, Henning Hermjakob, Claire O'Donovan, Maria Jesus Martin, Janet M. Thornton, Christoph Steinbeck
The EBI enzyme portal. Nucleic Acids Res. 41 (Database-Issue) (2013)
Tony E. Lewis, Ian Sillitoe, Antonina Andreeva, Tom L. Blundell, Daniel W. A. Buchan, Cyrus Chothia, Alison L. Cuff, Jose M. Dana, Ioannis Filippis, Julian Gough, Sarah Hunter, David T. Jones, Lawrence A. Kelley, Gerard J. Kleywegt, Federico Minneci, Alex L. Mitchell, Alexey G. Murzin, Bernardo Ochoa-Montaño, Owen J. L. Rackham, James Smith, Michael J. E. Sternberg, Sameer Velankar, Corin Yeats, Christine A. Orengo
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. Nucleic Acids Res. 41 (Database-Issue) (2013)
Jon Chambers, Mark Davies, Anna Gaulton, Anne Hersey, Sameer Velankar, Robert Petryszak, Janna Hastings, Louisa J. Bellis, Shaun McGlinchey, John P. Overington
UniChem: a unified chemical structure cross-referencing and identifier tracking system. J. Cheminformatics 5 (2013)
John Gómez, Leyla J. García, Gustavo A. Salazar, Jose M. Villaveces, Swanand P. Gore, Alexander García Castro, Maria Jesus Martin, Guillaume Launay, Rafael Alcántara, Noemi del-Toro, Marine Dumousseau, Sandra E. Orchard, Sameer Velankar, Henning Hermjakob, Chenggong Zong, Peipei Ping, Manuel Corpas, Rafael C. Jimenez
BioJS: an open source JavaScript framework for biological data visualization. Bioinform. 29 (8) (2013)
Sameer Velankar, Younes Alhroub, Christoph Best, Ségolène Caboche, Matthew J. Conroy, Jose M. Dana, Manuel A. Fernandez Montecelo, Glen van Ginkel, Adel Golovin, Swanand P. Gore, Aleksandras Gutmanas, Pauline Haslam, Pieter M. S. Hendrickx, E. Heuson, Miriam Hirshberg, Melford John, Ingvar C. Lagerstedt, Saqib Mir, Laurence E. Newman, Thomas J. Oldfield, Ardan Patwardhan, Luana Rinaldi, Gaurav Sahni, Eduardo Sanz-García, Sanchayita Sen, Robert A. Slowley, Antonio Suarez-Uruena, G. J. Swaminathan, Martyn F. Symmons, Wim F. Vranken, Michael E. Wainwright, Gerard J. Kleywegt
PDBe: Protein Data Bank in Europe. Nucleic Acids Res. 40 (Database-Issue) (2012)
Catherine L. Lawson, Matthew L. Baker, Christoph Best, Chunxiao Bi, Matthew T. Dougherty, Powei Feng, Glen van Ginkel, Batsal Devkota, Ingvar C. Lagerstedt, Steven J. Ludtke, Richard H. Newman, Thomas J. Oldfield, Ian Rees, Gaurav Sahni, Raul Sala, Sameer Velankar, Joe D. Warren, John D. Westbrook, Kim Henrick, Gerard J. Kleywegt, Helen M. Berman, Wah Chiu
EMDataBank.org: unified data resource for CryoEM. Nucleic Acids Res. 39 (Database-Issue) (2011)
Sameer Velankar, Younes Alhroub, Anaëlle Alili, Christoph Best, Harry Boutselakis, Ségolène Caboche, Matthew J. Conroy, Jose M. Dana, Glen van Ginkel, Adel Golovin, Swanand P. Gore, Aleksandras Gutmanas, Pauline Haslam, Miriam Hirshberg, Melford John, Ingvar C. Lagerstedt, Saqib Mir, Laurence E. Newman, Thomas J. Oldfield, Christopher J. Penkett, Jorge Pineda-Castillo, Luana Rinaldi, Gaurav Sahni, Grégoire Sawka, Sanchayita Sen, Robert A. Slowley, Alan W. Sousa da Silva, Antonio Suarez-Uruena, Jawahar Swaminathan, Martyn F. Symmons, Wim F. Vranken, Michael E. Wainwright, Gerard J. Kleywegt
PDBe: Protein Data Bank in Europe. Nucleic Acids Res. 39 (Database-Issue) (2011)
Kim Henrick, Zukang Feng, Wolfgang Bluhm, Dimitris Dimitropoulos, Jurgen F. Doreleijers, Shuchismita Dutta, Judith L. Flippen-Anderson, John M. C. Ionides, Chisa Kamada, Eugene Krissinel, Catherine L. Lawson, John L. Markley, Haruki Nakamura, Richard H. Newman, Yukiko Shimizu, Jawahar Swaminathan, Sameer Velankar, Jeramia Ory, Eldon L. Ulrich, Wim F. Vranken, John D. Westbrook, Reiko Yamashita, Huanwang Yang, Jasmine Young, Muhammed Yousufuddin, Helen M. Berman
Remediation of the protein data bank archive. Nucleic Acids Res. 36 (Database-Issue) (2008)