Wim F. Vranken

Publication Activity (10 Years)

Years Active: 2003-2023
Publications (10 Years): 23

Top Topics

Protein Interaction

Intrinsically Disordered

Top Venues

Nucleic Acids Res.

Briefings Bioinform.

Comput. Sci. Eng.

Publications

Joel Roca-Martínez, Hrishikesh Dhondge, Michael Sattler, Wim F. Vranken
Deciphering the RRM-RNA recognition code: A computational analysis. PLoS Comput. Biol. 19 (1) (2023)
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, Yi Jun Tang, Bin Liu, Claudio Mirabello, Björn Wallner, Burkhard Rost, Dagmar Ilzhöfer, Maria Littmann, Michael Heinzinger, Lea I M. Krautheimer, Michael Bernhofer, Liam J. McGuffin, Isabelle Callebaut, Tristan Bitard Feildel, Jian Liu, Jianlin Cheng, Zhiye Guo, Jinbo Xu, Sheng Wang, Nawar Malhis, Jörg Gsponer, Chol-Song Kim, Kun-Sop Han, Myong-Chol Ma, Lukasz A. Kurgan, Sina Ghadermarzi, Akila Katuwawala, Bi Zhao, Zhenling Peng, Zhonghua Wu, Gang Hu, Kui Wang, Md. Tamjidul Hoque, Md Wasi Ul Kabir, Michele Vendruscolo, Pietro Sormanni, Min Li, Fuhao Zhang, Pengzhen Jia, Yida Wang, Michail Yu. Lobanov, Oxana V. Galzitskaya, Wim F. Vranken, Adrián Díaz, Thomas Litfin, Yaoqi Zhou, Jack Hanson, Kuldip K. Paliwal, Zsuzsanna Dosztányi, Gábor Erdös, Silvio C. E. Tosatto, Damiano Piovesan
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins. Nucleic Acids Res. 51 (W1) (2023)
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)
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, Gustavo D. Parisi, Mónika Fuxreiter, Silvio C. E. Tosatto
MobiDB: intrinsically disordered proteins in 2021. Nucleic Acids Res. 49 (Database-Issue) (2021)
Rita Pancsa, Wim F. Vranken, Bálint Mészáros
Computational resources for identifying and describing proteins driving liquid-liquid phase separation. Briefings Bioinform. 22 (5) (2021)
François Ancien, Fabrizio Pucci, Wim F. Vranken, Marianne Rooman
MutaFrame - an interpretative visualization framework for deleteriousness prediction of missense variants in the human exome. Bioinform. 38 (1) (2021)
Luciano Porto Kagami, Gabriele Orlando, Daniele Raimondi, François Ancien, Bhawna Dixit, Jose Gavaldá-García, Pathmanaban Ramasamy, Joel Roca-Martínez, Konstantina Tzavella, Wim F. Vranken
b2bTools: online predictions for protein biophysical features and their conservation. Nucleic Acids Res. 49 (Webserver-Issue) (2021)
Gabriele Orlando, Alexandra Silva, Sandra Macedo-Ribeiro, Daniele Raimondi, Wim F. Vranken
Accurate prediction of protein beta-aggregation with generalized statistical potentials. Bioinform. 36 (7) (2020)
Gabriele Orlando, Daniele Raimondi, Luciano Porto Kagami, Wim F. Vranken
ShiftCrypt: a web server to understand and biophysically align proteins through their NMR chemical shift values. Nucleic Acids Res. 48 (Webserver-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)
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, Radoslav Davidovic, A. Keith Dunker, Arne Elofsson, Julien Gobeill, Nicolás S. González Foutel, Govindarajan Sudha, Mainak Guharoy, Tamás Horváth, Valentin Iglesias, Andrey V. Kajava, Orsolya P. Kovács, John Lamb, Matteo Lambrughi, Tamas Lazar, Jeremy Y. Leclercq, Emanuela Leonardi, Sandra Macedo-Ribeiro, Mauricio Macossay-Castillo, Emiliano Maiani, José A. Manso, Cristina Marino Buslje, Elizabeth Martínez-Pérez, Bálint Mészáros, Ivan Micetic, Giovanni Minervini, Nikoletta Murvai, Marco Necci, Christos A. Ouzounis, Mátyás Pajkos, Lisanna Paladin, Rita Pancsa, Elena Papaleo, Gustavo D. Parisi, Emilie Pasche, Pedro J. Barbosa Pereira, Vasilis J. Promponas, Jordi Pujols, Federica Quaglia, Patrick Ruch, Marco Salvatore, Éva Schád, Beáta Szabó, Tamás Szaniszló, Stella Tamana, Ágnes Tantos, Nevena Veljkovic, Salvador Ventura, Wim F. Vranken, Zsuzsanna Dosztányi, Peter Tompa, Silvio C. E. Tosatto, Damiano Piovesan
DisProt: intrinsic protein disorder annotation in 2020. Nucleic Acids Res. 48 (Database-Issue) (2020)
Gabriele Orlando, Daniele Raimondi, Francesco Tabaro, Francesco Codicè, Yves Moreau, Wim F. Vranken
Computational identification of prion-like RNA-binding proteins that form liquid phase-separated condensates. Bioinform. 35 (22) (2019)
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, Pietro Sormanni, Peter Tompa, Michele Vendruscolo, Wim F. Vranken, Silvio C. E. Tosatto
MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins. Nucleic Acids Res. 46 (Database-Issue) (2018)
Daniele Raimondi, Gabriele Orlando, Yves Moreau, Wim F. Vranken
Ultra-fast global homology detection with Discrete Cosine Transform and Dynamic Time Warping. Bioinform. 34 (18) (2018)
Guillaume Brysbaert, Kevin Lorgouilloux, Wim F. Vranken, Marc F. Lensink
RINspector: a Cytoscape app for centrality analyses and DynaMine flexibility prediction. Bioinform. 34 (2) (2018)
Mihaly Varadi, Greet De Baets, Wim F. Vranken, Peter Tompa, Rita Pancsa
AmyPro: a database of proteins with validated amyloidogenic regions. Nucleic Acids Res. 46 (Database-Issue) (2018)
Ibrahim Tanyalcin, Carla Al Assaf, Julien Ferté, François Ancien, Taushif Khan, Guillaume Smits, Marianne Rooman, Wim F. Vranken
Lexicon Visualization Library and JavaScript for Scientific Data Visualization. Comput. Sci. Eng. 20 (1) (2018)
Gabriele Orlando, Daniele Raimondi, Taushif Khan, Tom Lenaerts, Wim F. Vranken
SVM-dependent pairwise HMM: an application to protein pairwise alignments. Bioinform. 33 (24) (2017)
Qingzhen Hou, Paul F. G. De Geest, Wim F. Vranken, Jaap Heringa, K. Anton Feenstra
Seeing the trees through the forest: sequence-based homo- and heteromeric protein-protein interaction sites prediction using random forest. Bioinform. 33 (10) (2017)
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, András Hatos, Andrey V. Kajava, Lajos Kalmár, Emanuela Leonardi, Tamas Lazar, Sandra Macedo-Ribeiro, Mauricio Macossay-Castillo, Attila Meszaros, Giovanni Minervini, Nikoletta Murvai, Jordi Pujols, Daniel B. Roche, Edoardo Salladini, Éva Schád, Antoine Schramm, Beáta Szabó, Ágnes Tantos, Fiorella Tonello, Konstantinos D. Tsirigos, Nevena Veljkovic, Salvador Ventura, Wim F. Vranken, Per Warholm, Vladimir N. Uversky, A. Keith Dunker, Sonia Longhi, Peter Tompa, Silvio C. E. Tosatto
DisProt 7.0: a major update of the database of disordered proteins. Nucleic Acids Res. 45 (Database-Issue) (2017)
Daniele Raimondi, Ibrahim Tanyalcin, Julien Ferté, Andrea M. Gazzo, Gabriele Orlando, Tom Lenaerts, Marianne Rooman, Wim F. Vranken
DEOGEN2: prediction and interactive visualization of single amino acid variant deleteriousness in human proteins. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Rita Pancsa, Mihaly Varadi, Peter Tompa, Wim F. Vranken
Start2Fold: a database of hydrogen/deuterium exchange data on protein folding and stability. Nucleic Acids Res. 44 (Database-Issue) (2016)
Daniele Raimondi, Andrea M. Gazzo, Marianne Rooman, Tom Lenaerts, Wim F. Vranken
Multilevel biological characterization of exomic variants at the protein level significantly improves the identification of their deleterious effects. Bioinform. 32 (12) (2016)
Daniele Raimondi, Gabriele Orlando, Wim F. Vranken
Clustering-based model of cysteine co-evolution improves disulfide bond connectivity prediction and reduces homologous sequence requirements. Bioinform. 31 (8) (2015)
Elisa Cilia, Rita Pancsa, Peter Tompa, Tom Lenaerts, Wim F. Vranken
The DynaMine webserver: predicting protein dynamics from sequence. Nucleic Acids Res. 42 (Webserver-Issue) (2014)
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)
Jurgen F. Doreleijers, Wim F. Vranken, Christopher F. Schulte, John L. Markley, Eldon L. Ulrich, Gert Vriend, Geerten W. Vuister
NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB. Nucleic Acids Res. 40 (Database-Issue) (2012)
Tsjerk A. Wassenaar, Marc van Dijk, Nuno Loureiro-Ferreira, Gijs van der Schot, Sjoerd J. de Vries, Christophe Schmitz, Johan van der Zwan, Rolf Boelens, Andrea Giachetti, Lucio Ferella, Antonio Rosato, Ivano Bertini, Torsten Herrmann, Hendrik R. A. Jonker, Anurag Bagaria, Victor Jaravine, Peter Güntert, Harald Schwalbe, Wim F. Vranken, Jurgen F. Doreleijers, Gert Vriend, Geerten W. Vuister, Daniel Franke, Alexey Kikhney, Dmitri I. Svergun, Rasmus H. Fogh, John M. C. Ionides, Ernest D. Laue, Chris A. E. M. Spronk, Simonas Jurksa, Marco Verlato, Simone Badoer, Stefano Dal Pra, Mirco Mazzucato, Eric Frizziero, Alexandre M. J. J. Bonvin
WeNMR: Structural Biology on the Grid. J. Grid Comput. 10 (4) (2012)
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)
Tsjerk A. Wassenaar, Marc van Dijk, Nuno Loureiro-Ferreira, Gijs van der Schot, Sjoerd J. de Vries, Christophe Schmitz, Johan van der Zwan, Rolf Boelens, Andrea Giachetti, Lucio Ferella, Antonio Rosato, Ivano Bertini, Torsten Herrmann, Hendrik R. A. Jonker, Anurag Bagaria, Victor Jaravine, Peter Güntert, Harald Schwalbe, Wim F. Vranken, Jurgen F. Doreleijers, Gert Vriend, Geerten W. Vuister, Daniel Franke, Alexey Kikhney, Dmitri I. Svergun, Rasmus H. Fogh, John M. C. Ionides, Ernest D. Laue, Chris A. E. M. Spronk, Marco Verlato, Simone Badoer, Stefano Dal Pra, Mirco Mazzucato, Eric Frizziero, Alexandre M. J. J. Bonvin
WeNMR: Structural Biology on the Grid. IWSG-Life (2011)
Rasmus H. Fogh, Wayne Boucher, John M. C. Ionides, Wim F. Vranken, Tim J. Stevens, Ernest D. Laue
MEMOPS: Data modelling and automatic code generation.. J. Integr. Bioinform. 7 (3) (2010)
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, Thomas J. Oldfield, Anne Pajon, Christopher J. Penkett, Jorge Pineda-Castillo, Gaurav Sahni, Sanchayita Sen, Robert A. Slowley, Antonio Suarez-Uruena, Jawahar Swaminathan, Glen van Ginkel, Wim F. Vranken, Kim Henrick, Gerard J. Kleywegt
PDBe: Protein Data Bank in Europe. Nucleic Acids Res. 38 (Database-Issue) (2010)
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)
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
E-MSD: improving data deposition and structure quality. Nucleic Acids Res. 34 (Database-Issue) (2006)
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
A framework for scientific data modeling and automated software development. Bioinform. 21 (8) (2005)
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, Evgeny B. Krissinel, P. McNeil, Avi Naim, Richard H. Newman, Anne Pajon, Jorge Pineda, Abdel-Krim Rachedi, J. Copeland, Andrey Sitnov, Siamak Sobhany, Antonio Suarez-Uruena, G. J. Swaminathan, Mohammed Tagari, Swen Tromm, Wim F. Vranken, Kim Henrick
E-MSD: an integrated data resource for bioinformatics. Nucleic Acids Res. 32 (Database-Issue) (2004)
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, Richard H. Newman, Thomas J. Oldfield, Jorge Pineda, Abdel-Krim Rachedi, J. Copeland, Andrey Sitnov, Siamak Sobhany, Antonio Suarez-Uruena, Jawahar Swaminathan, Mohammed Tagari, John G. Tate, Swen Tromm, Samir S. Velankar, Wim F. Vranken
E-MSD: the European Bioinformatics Institute Macromolecular Structure Database. Nucleic Acids Res. 31 (1) (2003)