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)

A framework for scientific data modeling and automated software development. - Rasmus H. Fogh; Wayne Boucher; Wim F. Vranken; Anne Pajon; Tim J. Stevens; T. N. Bhat; John D. Westbrook; John M. C. Ionides; Ernest D. Laue (Bioinform., 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)

MEMOPS: Data modelling and automatic code generation.. - Rasmus H. Fogh; Wayne Boucher; John M. C. Ionides; Wim F. Vranken; Tim J. Stevens; Ernest D. Laue (J. Integr. Bioinform., 2010)

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)

WeNMR: Structural Biology on the Grid. - Tsjerk A. Wassenaar; Marc van Dijk; Nuno Loureiro-Ferreira; Gijs van der Schot; Sjoerd Jacob de Vries; Christophe Schmitz; Johan van der Zwan; Rolf Boelens; Andrea Giachetti 002; Lucio Ferella; Antonio Rosato; Ivano Bertini; et al. (IWSG-Life, 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)

WeNMR: Structural Biology on the Grid. - Tsjerk A. Wassenaar; Marc van Dijk; Nuno Loureiro-Ferreira; Gijs van der Schot; Sjoerd Jacob de Vries; Christophe Schmitz; Johan van der Zwan; Rolf Boelens; Andrea Giachetti 002; Lucio Ferella; Antonio Rosato; Ivano Bertini; et al. (J. Grid Comput., 2012)

NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB. - Jurgen F. Doreleijers; Wim F. Vranken; Christopher F. Schulte; John L. Markley; Eldon L. Ulrich; Gert Vriend; Geerten W. Vuister (Nucleic Acids Res., 2012)

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)

The DynaMine webserver: predicting protein dynamics from sequence. - Elisa Cilia; Rita Pancsa; Peter Tompa; Tom Lenaerts; Wim F. Vranken (Nucleic Acids Res., 2014)

Clustering-based model of cysteine co-evolution improves disulfide bond connectivity prediction and reduces homologous sequence requirements. - Daniele Raimondi; Gabriele Orlando; Wim F. Vranken (Bioinform., 2015)

Multilevel biological characterization of exomic variants at the protein level significantly improves the identification of their deleterious effects. - Daniele Raimondi; Andrea M. Gazzo; Marianne Rooman; Tom Lenaerts; Wim F. Vranken (Bioinform., 2016)

Start2Fold: a database of hydrogen/deuterium exchange data on protein folding and stability. - Rita Pancsa; Mihaly Varadi; Peter Tompa; Wim F. Vranken (Nucleic Acids Res., 2016)

Seeing the trees through the forest: sequence-based homo- and heteromeric protein-protein interaction sites prediction using random forest. - Qingzhen Hou; Paul F. G. De Geest; Wim F. Vranken; Jaap Heringa; K. Anton Feenstra (Bioinform., 2017)

SVM-dependent pairwise HMM: an application to protein pairwise alignments. - Gabriele Orlando; Daniele Raimondi; Taushif Khan; Tom Lenaerts; Wim F. Vranken (Bioinform., 2017)

DisProt 7.0: a major update of the database of disordered proteins. - Damiano Piovesan; Francesco Tabaro; Ivan Micetic; Marco Necci; Federica Quaglia; Christopher J. Oldfield; Maria Cristina Aspromonte; Norman E. Davey; Radoslav Davidovic; Zsuzsanna Dosztányi; Arne Elofsson; Alessandra Gasparini; et al. (Nucleic Acids Res., 2017)

DEOGEN2: prediction and interactive visualization of single amino acid variant deleteriousness in human proteins. - Daniele Raimondi; Ibrahim Tanyalcin; Julien Ferté; Andrea M. Gazzo; Gabriele Orlando; Tom Lenaerts; Marianne Rooman; Wim F. Vranken (Nucleic Acids Res., 2017)

RINspector: a Cytoscape app for centrality analyses and DynaMine flexibility prediction. - Guillaume Brysbaert; Kevin Lorgouilloux; Wim F. Vranken; Marc F. Lensink (Bioinform., 2018)

Ultra-fast global homology detection with Discrete Cosine Transform and Dynamic Time Warping. - Daniele Raimondi; Gabriele Orlando; Yves Moreau; Wim F. Vranken (Bioinform., 2018)

Lexicon Visualization Library and JavaScript for Scientific Data Visualization. - Ibrahim Tanyalcin; Carla Al Assaf; Julien Ferté; François Ancien; Taushif Khan; Guillaume Smits; Marianne Rooman; Wim F. Vranken (Comput. Sci. Eng., 2018)

MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins. - Damiano Piovesan; Francesco Tabaro; Lisanna Paladin; Marco Necci; Ivan Micetic; Carlo Camilloni; Norman E. Davey; Zsuzsanna Dosztányi; Bálint Mészáros; Alexander Miguel Monzon; Gustavo D. Parisi; Éva Schád; et al. (Nucleic Acids Res., 2018)

AmyPro: a database of proteins with validated amyloidogenic regions. - Mihaly Varadi; Greet De Baets; Wim F. Vranken; Peter Tompa; Rita Pancsa (Nucleic Acids Res., 2018)

Computational identification of prion-like RNA-binding proteins that form liquid phase-separated condensates. - Gabriele Orlando; Daniele Raimondi; Francesco Tabaro; Francesco Codicè; Yves Moreau; Wim F. Vranken (Bioinform., 2019)

Accurate prediction of protein beta-aggregation with generalized statistical potentials. - Gabriele Orlando; Alexandra Silva 004; Sandra Macedo-Ribeiro; Daniele Raimondi; Wim F. Vranken (Bioinform., 2020)

DisProt: intrinsic protein disorder annotation in 2020. - András Hatos; Borbála Hajdu-Soltész; Alexander Miguel Monzon; Nicolas Palopoli; Lucía Álvarez; Burcu Aykaç Fas; Claudio Bassot; Guillermo I. Benítez; Martina Bevilacqua; Anastasia Chasapi; Lucía B. Chemes; Norman E. Davey; et al. (Nucleic Acids Res., 2020)

ShiftCrypt: a web server to understand and biophysically align proteins through their NMR chemical shift values. - Gabriele Orlando; Daniele Raimondi; Luciano Porto Kagami; Wim F. Vranken (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)

Computational resources for identifying and describing proteins driving liquid-liquid phase separation. - Rita Pancsa; Wim F. Vranken; Bálint Mészáros (Briefings Bioinform., 2021)

MutaFrame - an interpretative visualization framework for deleteriousness prediction of missense variants in the human exome. - François Ancien; Fabrizio Pucci; Wim F. Vranken; Marianne Rooman (Bioinform., 2021)

b2bTools: online predictions for protein biophysical features and their conservation. - Luciano Porto Kagami; Gabriele Orlando; Daniele Raimondi; François Ancien; Bhawna Dixit; Jose Gavaldá-García; Pathmanaban Ramasamy; Joel Roca-Martínez; Konstantina Tzavella; Wim F. Vranken (Nucleic Acids Res., 2021)

MobiDB: intrinsically disordered proteins in 2021. - Damiano Piovesan; Marco Necci; Nahuel Escobedo; Alexander Miguel Monzon; András Hatos; Ivan Micetic; Federica Quaglia; Lisanna Paladin; Pathmanaban Ramasamy; Zsuzsanna Dosztányi; Wim F. Vranken; Norman E. Davey; et al. (Nucleic Acids Res., 2021)

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)

Deciphering the RRM-RNA recognition code: A computational analysis. - Joel Roca-Martínez; Hrishikesh Dhondge; Michael Sattler; Wim F. Vranken (PLoS Comput. Biol., 2023)

CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins. - Alessio Del Conte; Adel Bouhraoua; Mahta Mehdiabadi; Damiano Clementel; Alexander Miguel Monzon; Alex S. Holehouse; Daniel A. Griffith; Ryan J. Emenecker; Ashwini Patil; Ronesh Sharma; Tatsuhiko Tsunoda; Alok Sharma; et al. (Nucleic Acids Res., 2023)

Combining evolution and protein language models for an interpretable cancer driver mutation prediction with D2Deep. - Konstantina Tzavella; Adrián Díaz; Catharina Olsen; Wim F. Vranken (Briefings Bioinform., 2024)