E-MSD: the European Bioinformatics Institute Macromolecular Structure Database. - Harry Boutselakis; Dimitris Dimitropoulos; Joël Fillon; Adel Golovin; Kim Henrick; A. Hussain; John M. C. Ionides; Melford John; Peter A. Keller; Evgeny B. Krissinel; P. McNeil; Avi Naim; et al. (Nucleic Acids Res., 2003)

E-MSD: an integrated data resource for bioinformatics. - Adel Golovin; Thomas J. Oldfield; John G. Tate; Samir S. Velankar; Geoffrey J. Barton; Harry Boutselakis; Dimitris Dimitropoulos; Joël Fillon; A. Hussain; John M. C. Ionides; Melford John; Peter A. Keller; et al. (Nucleic Acids Res., 2004)

SOAP-based services provided by the European Bioinformatics Institute. - Sharmila Pillai; Ville Silventoinen; Kimmo Kallio; M. Senger; Siamak Sobhany; John G. Tate; Samir S. Velankar; Adel Golovin; Kim Henrick; Peter M. Rice; Peter Stoehr; Rodrigo Lopez (Nucleic Acids Res., 2005)

E-MSD: an integrated data resource for bioinformatics. - Samir S. Velankar; P. McNeil; Virginie Mittard-Runte; A. Suarez; Daniel Barrell; Rolf Apweiler; Kim Henrick (Nucleic Acids Res., 2005)

E-MSD: improving data deposition and structure quality. - Mohammed Tagari; John G. Tate; G. J. Swaminathan; Richard H. Newman; Avi Naim; Wim F. Vranken; A. Kapopoulou; A. Hussain; Joël Fillon; Kim Henrick; Samir S. Velankar (Nucleic Acids Res., 2006)

Remediation of the protein data bank archive. - 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; et al. (Nucleic Acids Res., 2008)

PDBe: Protein Data Bank in Europe. - Samir S. Velankar; Christoph Best; B. Beuth; Harry Boutselakis; N. Cobley; Alan W. Sousa da Silva; Dimitris Dimitropoulos; Adel Golovin; Miriam Hirshberg; Melford John; Evgeny B. Krissinel; Richard H. Newman; et al. (Nucleic Acids Res., 2010)

EMDataBank.org: unified data resource for CryoEM. - 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; et al. (Nucleic Acids Res., 2011)

PDBe: Protein Data Bank in Europe. - 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; et al. (Nucleic Acids Res., 2011)

PDBe: Protein Data Bank in Europe. - 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; et al. (Nucleic Acids Res., 2012)

BioJS: an open source JavaScript framework for biological data visualization. - 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; et al. (Bioinform., 2013)

UniChem: a unified chemical structure cross-referencing and identifier tracking system. - Jon Chambers; Mark Davies; Anna Gaulton; Anne Hersey; Sameer Velankar; Robert Petryszak; Janna Hastings; Louisa J. Bellis; Shaun McGlinchey; John P. Overington (J. Cheminformatics, 2013)

The EBI enzyme portal. - 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; et al. (Nucleic Acids Res., 2013)

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. - 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; et al. (Nucleic Acids Res., 2013)

SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. - 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 (Nucleic Acids Res., 2013)

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; et al. (Nucleic Acids Res., 2014)

The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank. - John D. Westbrook; Chenghua Shao; Zukang Feng; Marina Zhuravleva; Sameer Velankar; Jasmine Young (Bioinform., 2015)

Genome3D: exploiting structure to help users understand their sequences. - 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; et al. (Nucleic Acids Res., 2015)

The complex portal - an encyclopaedia of macromolecular complexes. - 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; et al. (Nucleic Acids Res., 2015)

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; et al. (Nucleic Acids Res., 2016)

Mol*: Towards a Common Library and Tools for Web Molecular Graphics. - David Sehnal; Alexander S. Rose; Jaroslav Koca; Stephen K. Burley; Sameer Velankar (MolVa@EuroVis, 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; et al. (Database J. Biol. Databases Curation, 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; et al. (Nucleic Acids Res., 2018)

Finding enzyme cofactors in Protein Data Bank. - Abhik Mukhopadhyay; Neera Borkakoti; Lukás Pravda; Jonathan D. Tyzack; Janet M. Thornton; Sameer Velankar (Bioinform., 2019)

SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins. - Jose M. Dana; Aleksandras Gutmanas; Nidhi Tyagi; Guoying Qi; Claire O'Donovan; Maria Jesus Martin; Sameer Velankar (Nucleic Acids Res., 2019)

The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences. - 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; et al. (Bioinform., 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; et al. (Nucleic Acids Res., 2020)

Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation. - 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; et al. (Nucleic Acids Res., 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; et al. (Nucleic Acids Res., 2020)

BinaryCIF and CIFTools - Lightweight, efficient and extensible macromolecular data management. - David Sehnal; Sebastian Bittrich; Sameer Velankar; Jaroslav Koca; Radka Svobodová Vareková; Stephen K. Burley; Alexander S. Rose (PLoS Comput. Biol., 2020)

The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies. - Vaishali P. Waman; Neeladri Sen; Mihaly Varadi; Antoine Daina; Shoshana J. Wodak; Vincent Zoete; Sameer Velankar; Christine A. Orengo (Briefings Bioinform., 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)

PDBeCIF: an open-source mmCIF/CIF parsing and processing package. - Glen van Ginkel; Lukás Pravda; Jose M. Dana; Mihaly Varadi; Peter A. Keller; Stephen Anyango; Sameer Velankar (BMC Bioinform., 2021)

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. - David Sehnal; Sebastian Bittrich; Mandar S. Deshpande; Radka Svobodová Vareková; Karel Berka; Václav Bazgier; Sameer Velankar; Stephen K. Burley; Jaroslav Koca; Alexander S. Rose (Nucleic Acids Res., 2021)

Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs. - Neeladri Sen; Ivan Anishchenko; Nicola Bordin; Ian Sillitoe; Sameer Velankar; David Baker 001; Christine A. Orengo (Briefings Bioinform., 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; et al. (Nucleic Acids Res., 2022)

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. - 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; et al. (Nucleic Acids Res., 2022)

EMBL's European Bioinformatics Institute (EMBL-EBI) in 2022. - 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; et al. (Nucleic Acids Res., 2023)

PDBImages: a command-line tool for automated macromolecular structure visualization. - Adam Midlik; Sreenath Nair; Stephen Anyango; Mandar S. Deshpande; David Sehnal; Mihaly Varadi; Sameer Velankar (Bioinform., 2023)

PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank. - Ibrahim Roshan Kunnakkattu; Preeti Choudhary; Lukás Pravda; Nurul Nadzirin; Oliver S. Smart; Qi Yuan; Stephen Anyango; Sreenath Nair; Mihaly Varadi; Sameer Velankar (J. Cheminformatics, 2023)

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 002; Ahsan Tanweer; Mihaly Varadi; John D. Westbrook; Jasmine Young; et al. (Database J. Biol. Databases Curation, 2024)