Fine specificity of antigen binding to two class I major histocompatibility proteins (B*2705 and B*2703) differing in a single amino acid residue. - Didier Rognan; Stefan Krebs; Oliver Kuonen; José R. Lamas; José A. López de Castro; Gerd Folkers (J. Comput. Aided Mol. Des., 1997)

Modeling the interactions of a peptide-major histocompatibility class I ligand with its receptors. II. Cross-reaction between a monoclonal antibody and two alpha-beta T cell receptors. - Didier Rognan; Jan Engberg; Anette Stryhn; Peter Sejer Andersen; Søren Buus (J. Comput. Aided Mol. Des., 2000)

Modeling the interactions of a peptide-major histocompatibility class I ligand with its receptors. I. Recognition by two alpha-beta T cell receptors. - Didier Rognan; Anette Stryhn; Lars Fugger; Stig Lyngbæk; Jan Engberg; Peter Sejer Andersen; Søren Buus (J. Comput. Aided Mol. Des., 2000)

NMR-restrained docking of a peptidic inhibitor to the N-terminal domain of the phosphoenolpyruvate: sugar phosphotransferase enzyme I. - Didier Rognan; Seema Mukhija; Gerd Folkers; Oliver Zerbe (J. Comput. Aided Mol. Des., 2001)

Recovery of known T-cell epitopes by computational scanning of a viral genome. - Antoine Logean; Didier Rognan (J. Comput. Aided Mol. Des., 2002)

High-Throughput Modeling of Human G-Protein Coupled Receptors: Amino Acid Sequence Alignment, Three-Dimensional Model Building, and Receptor Library Screening. - Caterina Bissantz; Antoine Logean; Didier Rognan (J. Chem. Inf. Model., 2004)

sc-PDB: an Annotated Database of Druggable Binding Sites from the Protein Data Bank. - Esther Kellenberger; Pascal Muller; Claire Schalon; Guillaume Bret; Nicolas Foata; Didier Rognan (J. Chem. Inf. Model., 2006)

Assessing the Scaffold Diversity of Screening Libraries. - Mireille Krier; Guillaume Bret; Didier Rognan (J. Chem. Inf. Model., 2006)

Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints. - Gilles Marcou; Didier Rognan (J. Chem. Inf. Model., 2007)

Hot-Spots-Guided Receptor-Based Pharmacophores (HS-Pharm): A Knowledge-Based Approach to Identify Ligand-Anchoring Atoms in Protein Cavities and Prioritize Structure-Based Pharmacophores. - Caterina Barillari; Gilles Marcou; Didier Rognan (J. Chem. Inf. Model., 2008)

Ranking Targets in Structure-Based Virtual Screening of Three-Dimensional Protein Libraries: Methods and Problems. - Esther Kellenberger; Nicolas Foata; Didier Rognan (J. Chem. Inf. Model., 2008)

Development and Validation of a Novel Protein-Ligand Fingerprint To Mine Chemogenomic Space: Application to G Protein-Coupled Receptors and Their Ligands. - Nathanael Weill; Didier Rognan (J. Chem. Inf. Model., 2009)

Alignment-Free Ultra-High-Throughput Comparison of Druggable Protein-Ligand Binding Sites. - Nathanael Weill; Didier Rognan (J. Chem. Inf. Model., 2010)

sc-PDB: a database for identifying variations and multiplicity of 'druggable' binding sites in proteins. - Jamel Meslamani; Didier Rognan; Esther Kellenberger (Bioinform., 2011)

Enhancing the Accuracy of Chemogenomic Models with a Three-Dimensional Binding Site Kernel. - Jamel Meslamani; Didier Rognan (J. Chem. Inf. Model., 2011)

Comparison and Druggability Prediction of Protein-Ligand Binding Sites from Pharmacophore-Annotated Cavity Shapes. - Jérémy Desaphy; Karima Azdimousa; Esther Kellenberger; Didier Rognan (J. Chem. Inf. Model., 2012)

Protein-Ligand-Based Pharmacophores: Generation and Utility Assessment in Computational Ligand Profiling. - Jamel Meslamani; Jiabo Li; Jon M. Sutter; Adrian Stevens; Hugues-Olivier Bertrand; Didier Rognan (J. Chem. Inf. Model., 2012)

Structural Insights into the Molecular Basis of the Ligand Promiscuity. - Noé Sturm; Jérémy Desaphy; Ronald J. Quinn; Didier Rognan; Esther Kellenberger (J. Chem. Inf. Model., 2012)

Predicting Ligand Binding Modes from Neural Networks Trained on Protein-Ligand Interaction Fingerprints. - Vladimir I. Chupakhin; Gilles Marcou; Igor I. Baskin; Alexandre Varnek; Didier Rognan (J. Chem. Inf. Model., 2013)

Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs. - Jérémy Desaphy; Eric Raimbaud; Pierre Ducrot; Didier Rognan (J. Chem. Inf. Model., 2013)

Computational Profiling of Bioactive Compounds Using a Target-Dependent Composite Workflow. - Jamel Meslamani; Ricky Bhajun; François Martz; Didier Rognan (J. Chem. Inf. Model., 2013)

sc-PDB-Frag: A Database of Protein-Ligand Interaction Patterns for Bioisosteric Replacements. - Jérémy Desaphy; Didier Rognan (J. Chem. Inf. Model., 2014)

Beware of Machine Learning-Based Scoring Functions - On the Danger of Developing Black Boxes. - Joffrey Gabel; Jérémy Desaphy; Didier Rognan (J. Chem. Inf. Model., 2014)

IChemPIC: A Random Forest Classifier of Biological and Crystallographic Protein-Protein Interfaces. - Franck Da Silva; Jérémy Desaphy; Guillaume Bret; Didier Rognan (J. Chem. Inf. Model., 2015)

sc-PDB: a 3D-database of ligandable binding sites - 10 years on. - Jérémy Desaphy; Guillaume Bret; Didier Rognan; Esther Kellenberger (Nucleic Acids Res., 2015)

Docking pose selection by interaction pattern graph similarity: application to the D3R grand challenge 2015. - Inna Slynko; Franck Da Silva; Guillaume Bret; Didier Rognan (J. Comput. Aided Mol. Des., 2016)

Ranking docking poses by graph matching of protein-ligand interactions: lessons learned from the D3R Grand Challenge 2. - Priscila da Silva Figueiredo Celestino Gomes; Franck Da Silva; Guillaume Bret; Didier Rognan (J. Comput. Aided Mol. Des., 2018)

Unsupervised Classification of G-Protein Coupled Receptors and Their Conformational States Using IChem Intramolecular Interaction Patterns. - Florian Koensgen; Franck Da Silva; Didier Rognan; Esther Kellenberger (J. Chem. Inf. Model., 2019)

All in One: Cavity Detection, Druggability Estimate, Cavity-Based Pharmacophore Perception, and Virtual Screening. - Viet-Khoa Tran-Nguyen; Franck Da Silva; Guillaume Bret; Didier Rognan (J. Chem. Inf. Model., 2019)

LIT-PCBA: An Unbiased Data Set for Machine Learning and Virtual Screening. - Viet-Khoa Tran-Nguyen; Célien Jacquemard; Didier Rognan (J. Chem. Inf. Model., 2020)

Unexpected similarity between HIV-1 reverse transcriptase and tumor necrosis factor binding sites revealed by computer vision. - Merveille K. I. Eguida; Didier Rognan (J. Cheminformatics, 2021)

True Accuracy of Fast Scoring Functions to Predict High-Throughput Screening Data from Docking Poses: The Simpler the Better. - Viet-Khoa Tran-Nguyen; Guillaume Bret; Didier Rognan (J. Chem. Inf. Model., 2021)

Subpocket Similarity-Based Hit Identification for Challenging Targets: Application to the WDR Domain of LRRK2. - Merveille K. I. Eguida; Guillaume Bret; François Sindt; Fengling Li; Irene Chau; Suzanne Ackloo; Cheryl H. Arrowsmith; Albina Bolotokova; Pegah Ghiabi; Elisa Gibson; Levon Halabelian; Scott Houliston; et al. (J. Chem. Inf. Model., 2024)

CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson's Disease Associated Protein. - Fengling Li; Suzanne Ackloo; Cheryl H. Arrowsmith; Fuqiang Ban; Christopher J. Barden; Hartmut Beck; Jan Beránek; Francois Berenger; Albina Bolotokova; Guillaume Bret; Marko Breznik; Emanuele Carosati; et al. (J. Chem. Inf. Model., 2024)

Active Learning to Select the Most Suitable Reagents and One-Step Organic Chemistry Reactions for Prioritizing Target-Specific Hits from Ultralarge Chemical Spaces. - Vladimir Kozyrev; François Sindt; Didier Rognan (J. Chem. Inf. Model., 2025)

On the Difficulty to Rescore Hits from Ultralarge Docking Screens. - François Sindt; Guillaume Bret; Didier Rognan (J. Chem. Inf. Model., 2025)