Joost Schymkowitz

35 papers Journal 34Unranked 1

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	AXZ viewer: a web application to visualize unprocessed AFM-IR data. Bioinform. Wouter Duverger, Georg Ramer, Nikolaos N. Louros, Joost Schymkowitz, Frederic Rousseau
2025	J	`jnl`	Charting the structure-sequence landscape of light chain amyloids. Bioinform. Gabriele Orlando, Rodrigo Gallardo, Alicia Colla, Joost Schymkowitz, Frederic Rousseau
2025	J	`jnl`	FoldX force field revisited, an improved version. Bioinform. Javier Delgado, Raul Reche, Damiano Cianferoni, Gabriele Orlando, Rob van der Kant, Frederic Rousseau, Joost Schymkowitz, Luis Serrano
2024	J	`jnl`	CORDAX web server: an online platform for the prediction and 3D visualization of aggregation motifs in protein sequences. Bioinform. Nikolaos N. Louros, Frederic Rousseau, Joost Schymkowitz
2024	J	`jnl`	Integrating physics in deep learning algorithms: a force field as a PyTorch module. Bioinform. Gabriele Orlando, Luis Serrano, Joost Schymkowitz, Frederic Rousseau
2023	J	`jnl`	SNPeffect 5.0: large-scale structural phenotyping of protein coding variants extracted from next-generation sequencing data using AlphaFold models. BMC Bioinform. Kobe Janssen, Ramon Duran-Romaña, Guy Bottu, Mainak Guharoy, Alexander Botzki, Frederic Rousseau, Joost Schymkowitz
2022	J	`jnl`	StAmP-DB: a platform for structures of polymorphic amyloid fibril cores. Bioinform. Nikolaos N. Louros, Rob van der Kant, Joost Schymkowitz, Frederic Rousseau
2021	J	`jnl`	In silico prediction of in vitro protein liquid-liquid phase separation experiments outcomes with multi-head neural attention. Bioinform. Daniele Raimondi, Gabriele Orlando, Emiel Michiels, Donya Pakravan, Anna Bratek-Skicki, Ludo Van Den Bosch, Yves Moreau, Frederic Rousseau, Joost Schymkowitz
2020	J	`jnl`	Protein Homeostasis Database: protein quality control in E.coli. Bioinform. Reshmi Ramakrishnan, Bert Houben, Lukasz Kreft, Alexander Botzki, Joost Schymkowitz, Frederic Rousseau
2020	J	`jnl`	WALTZ-DB 2.0: an updated database containing structural information of experimentally determined amyloid-forming peptides. Nucleic Acids Res. Nikolaos N. Louros, Katerina Konstantoulea, Matthias De vleeschouwer, Meine Ramakers, Joost Schymkowitz, Frederic Rousseau
2019	J	`jnl`	Differential proteostatic regulation of insoluble and abundant proteins. Bioinform. Reshmi Ramakrishnan, Bert Houben, Frederic Rousseau, Joost Schymkowitz
2016	J	`jnl`	From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors. PLoS Comput. Biol. Ana Zafra Ruano, Elisa Cilia, José R. Couceiro, Javier Ruiz Sanz, Joost Schymkowitz, Frederic Rousseau, Irene Luque, Tom Lenaerts
2015	J	`jnl`	Increased Aggregation Is More Frequently Associated to Human Disease-Associated Mutations Than to Neutral Polymorphisms. PLoS Comput. Biol. Greet De Baets, Loic Van Doorn, Frederic Rousseau, Joost Schymkowitz
2015	J	`jnl`	PrionW: a server to identify proteins containing glutamine/asparagine rich prion-like domains and their amyloid cores. Nucleic Acids Res. Rafael Zambrano, Oscar Conchillo-Solé, Valentin Iglesias, Ricard Illa, Frederic Rousseau, Joost Schymkowitz, Raimon Sabate, Xavier Daura, Salvador Ventura
2015	J	`jnl`	Solubis: optimize your protein. Bioinform. Greet De Baets, Joost J. J. van Durme, Rob van der Kant, Joost Schymkowitz, Frederic Rousseau
2015	J	`jnl`	WALTZ-DB: a benchmark database of amyloidogenic hexapeptides. Bioinform. Jacinte Beerten, Joost J. J. van Durme, Rodrigo Gallardo, Emidio Capriotti, Louise C. Serpell, Frederic Rousseau, Joost Schymkowitz
2015	J	`jnl`	What Makes a Protein Sequence a Prion? PLoS Comput. Biol. Raimon Sabate, Frederic Rousseau, Joost Schymkowitz, Salvador Ventura
2013	J	`jnl`	Motif Discovery with Data Mining in 3D protein Structure Databases: Discovery, Validation and Prediction of the U-Shape zinc binding ("Huf-zinc") Motif. J. Bioinform. Comput. Biol. Sebastian Maurer-Stroh, He Gao, Hao Han, Lies Baeten, Joost Schymkowitz, Frederic Rousseau, Louxin Zhang, Frank Eisenhaber
2012	J	`jnl`	SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants. Nucleic Acids Res. Greet De Baets, Joost J. J. van Durme, Joke Reumers, Sebastian Maurer-Stroh, Peter Vanhee, Joaquín Dopazo, Joost Schymkowitz, Frederic Rousseau
2011	J	`jnl`	A graphical interface for the FoldX forcefield. Bioinform. Joost J. J. van Durme, Javier Delgado Blanco, Francois Stricher, Luis Serrano, Joost Schymkowitz, Frederic Rousseau
2011	J	`jnl`	An Evolutionary Trade-Off between Protein Turnover Rate and Protein Aggregation Favors a Higher Aggregation Propensity in Fast Degrading Proteins. PLoS Comput. Biol. Greet De Baets, Joke Reumers, Javier Delgado Blanco, Joaquín Dopazo, Joost Schymkowitz, Frederic Rousseau
2011	J	`jnl`	BriX: a database of protein building blocks for structural analysis, modeling and design. Nucleic Acids Res. Peter Vanhee, Erik Verschueren, Lies Baeten, Francois Stricher, Luis Serrano, Frederic Rousseau, Joost Schymkowitz
2010	J	`jnl`	Modeling protein-peptide interactions using protein fragments: fitting the pieces? BMC Bioinform. Peter Vanhee, Francois Stricher, Lies Baeten, Erik Verschueren, Luis Serrano, Frederic Rousseau, Joost Schymkowitz
2010	J	`jnl`	PepX: a structural database of non-redundant protein-peptide complexes. Nucleic Acids Res. Peter Vanhee, Joke Reumers, Francois Stricher, Lies Baeten, Luis Serrano, Joost Schymkowitz, Frederic Rousseau
2009	J	`jnl`	Accurate Prediction of DnaK-Peptide Binding via Homology Modelling and Experimental Data. PLoS Comput. Biol. Joost J. J. van Durme, Sebastian Maurer-Stroh, Rodrigo Gallardo, Hannah Wilkinson, Frederic Rousseau, Joost Schymkowitz
2009	J	`jnl`	Information theoretical quantification of cooperativity in signalling complexes. BMC Syst. Biol. Tom Lenaerts, Jesper Ferkinghoff-Borg, Joost Schymkowitz, Frederic Rousseau
2009	J	`jnl`	Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations. BMC Bioinform. Joke Reumers, Joost Schymkowitz, Frederic Rousseau
2008	J	`jnl`	Genome-Wide Prediction of SH2 Domain Targets Using Structural Information and the FoldX Algorithm. PLoS Comput. Biol. Ignacio E. Sánchez, Pedro Beltrão, Francois Stricher, Joost Schymkowitz, Jesper Ferkinghoff-Borg, Frederic Rousseau, Luis Serrano
2008	J	`jnl`	Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases. Nucleic Acids Res. Joke Reumers, Lucía Conde, Ignacio Medina, Sebastian Maurer-Stroh, Joost J. J. van Durme, Joaquín Dopazo, Frederic Rousseau, Joost Schymkowitz
2008	J	`jnl`	Reconstruction of Protein Backbones from the BriX Collection of Canonical Protein Fragments. PLoS Comput. Biol. Lies Baeten, Joke Reumers, Vicente Tur, François Stricher, Tom Lenaerts, Luis Serrano, Frederic Rousseau, Joost Schymkowitz
2008	—	`conf`	Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations. AIMM Joke Reumers, Joost Schymkowitz, Frederic Rousseau
2006	J	`jnl`	PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes. Nucleic Acids Res. Lucía Conde, Juan M. Vaquerizas, Hernán Dopazo, Leonardo Arbiza, Joke Reumers, Frederic Rousseau, Joost Schymkowitz, Joaquín Dopazo
2006	J	`jnl`	SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs. Bioinform. Joke Reumers, Sebastian Maurer-Stroh, Joost Schymkowitz, Frederic Rousseau
2005	J	`jnl`	SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs. Nucleic Acids Res. Joke Reumers, Joost Schymkowitz, Jesper Ferkinghoff-Borg, Francois Stricher, Luis Serrano, Frederic Rousseau
2005	J	`jnl`	The FoldX web server: an online force field. Nucleic Acids Res. Joost Schymkowitz, Jesper Borg, Francois Stricher, Robby Nys, Frederic Rousseau, Luis Serrano