Modeling Antibody Side Chain Conformations Using Heuristic Database Search. - David W. Ritchie; Graham J. L. Kemp (ISMB, 1997)

Fast computation, rotation, and comparison of low resolution spherical harmonic molecular surfaces. - David W. Ritchie; Graham J. L. Kemp (J. Comput. Chem., 1999)

Modeling the Structural Basis of Human CCR5 Chemokine Receptor Function: From Homology Model Building and Molecular Dynamics Validation to Agonist and Antagonist Docking. - Alessandra Fano; David W. Ritchie; Antonio Carrieri (J. Chem. Inf. Model., 2006)

Toward High Throughput 3D Virtual Screening Using Spherical Harmonic Surface Representations. - Lazaros Mavridis; Brian D. Hudson; David W. Ritchie (J. Chem. Inf. Model., 2007)

Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions. - David W. Ritchie; Dima Kozakov; Sandor Vajda (Bioinform., 2008)

Clustering and Classifying Diverse HIV Entry Inhibitors Using a Novel Consensus Shape-Based Virtual Screening Approach: Further Evidence for Multiple Binding Sites within the CCR5 Extracellular Pocket. - Violeta I. Pérez-Nueno; David W. Ritchie; José I. Borrell; Jordi Teixidó (J. Chem. Inf. Model., 2008)

Comparison of Ligand-Based and Receptor-Based Virtual Screening of HIV Entry Inhibitors for the CXCR4 and CCR5 Receptors Using 3D Ligand Shape Matching and Ligand-Receptor Docking. - Violeta I. Pérez-Nueno; David W. Ritchie; Obdulia Rabal; Rosalia Pascual; José I. Borrell; Jordi Teixidó (J. Chem. Inf. Model., 2008)

Discovery of Novel HIV Entry Inhibitors for the CXCR4 Receptor by Prospective Virtual Screening. - Violeta I. Pérez-Nueno; Sofia Pettersson; David W. Ritchie; José I. Borrell; Jordi Teixidó (J. Chem. Inf. Model., 2009)

SHREC'10 Track: Protein Model Classification. - Lazaros Mavridis; Vishwesh Venkatraman; David W. Ritchie; Naoto Morikawa; Rumen Andonov; Alexandre Cornu; Noël Malod-Dognin; Jacques Nicolas; Maja Temerinac-Ott; Marco Reisert; Hans Burkhardt; Apostolos Axenopoulos; et al. (3DOR@Eurographics, 2010)

Using Graphics Processors to Accelerate Protein Docking Calculations. - David W. Ritchie; Vishwesh Venkatraman; Lazaros Mavridis (HealthGrid, 2010)

3D-Blast: 3D Protein Structure Alignment, Comparison, and Classification Using Spherical Polar Fourier Correlations. - Lazaros Mavridis; David W. Ritchie (Pacific Symposium on Biocomputing, 2010)

Ultra-fast FFT protein docking on graphics processors. - David W. Ritchie; Vishwesh Venkatraman (Bioinform., 2010)

Comprehensive Comparison of Ligand-Based Virtual Screening Tools Against the DUD Data set Reveals Limitations of Current 3D Methods. - Vishwesh Venkatraman; Violeta I. Pérez-Nueno; Lazaros Mavridis; David W. Ritchie (J. Chem. Inf. Model., 2010)

HexServer: an FFT-based protein docking server powered by graphics processors. - Gary Macindoe; Lazaros Mavridis; Vishwesh Venkatraman; Marie-Dominique Devignes; David W. Ritchie (Nucleic Acids Res., 2010)

Algorithmes Haute-Performance pour la Reconnaissance de Formes Moléculaires. (High Performance Algorithms for Molecular Shape Recognition). - David W. Ritchie (2011)

Using Kendall-τ Meta-Bagging to Improve Protein-Protein Docking Predictions. - Jérôme Azé; Thomas Bourquard; Sylvie Hamel; Anne Poupon; David W. Ritchie (PRIB, 2011)

Spatial clustering of protein binding sites for template based protein docking. - Anisah W. Ghoorah; Marie-Dominique Devignes; Malika Smaïl-Tabbone; David W. Ritchie (Bioinform., 2011)

Predicting drug polypharmacology using a novel surface property similarity-based approach. - Violeta I. Pérez-Nueno; Vishwesh Venkatraman; Lazaros Mavridis; David W. Ritchie (J. Cheminformatics, 2011)

Using Consensus-Shape Clustering To Identify Promiscuous Ligands and Protein Targets and To Choose the Right Query for Shape-Based Virtual Screening. - Violeta I. Pérez-Nueno; David W. Ritchie (J. Chem. Inf. Model., 2011)

Fast protein structure alignment using Gaussian overlap scoring of backbone peptide fragment similarity. - David W. Ritchie; Anisah W. Ghoorah; Lazaros Mavridis; Vishwesh Venkatraman (Bioinform., 2012)

Predicting Multi-Component Protein Assemblies Using an Ant Colony Approach. - Vishwesh Venkatraman; David W. Ritchie (Int. J. Swarm Intell. Res., 2012)

Detecting Drug Promiscuity Using Gaussian Ensemble Screening. - Violeta I. Pérez-Nueno; Vishwesh Venkatraman; Lazaros Mavridis; David W. Ritchie (J. Chem. Inf. Model., 2012)

GES Polypharmacology Fingerprints: A Novel Approach for Drug Repositioning. - Violeta I. Pérez-Nueno; Arnaud Sinan Karaboga; Michel Souchet; David W. Ritchie (J. Chem. Inf. Model., 2014)

KBDOCK 2013: a spatial classification of 3D protein domain family interactions. - Anisah W. Ghoorah; Marie-Dominique Devignes; Malika Smaïl-Tabbone; David W. Ritchie (Nucleic Acids Res., 2014)

GESSE: Predicting Drug Side Effects from Drug-Target Relationships. - Violeta I. Pérez-Nueno; Michel Souchet; Arnaud Sinan Karaboga; David W. Ritchie (J. Chem. Inf. Model., 2015)

PEPSI-Dock: a detailed data-driven protein-protein interaction potential accelerated by polar Fourier correlation. - Émilie Neveu; David W. Ritchie; Petr Popov; Sergei Grudinin (Bioinform., 2016)

Calculating and scoring high quality multiple flexible protein structure alignments. - David W. Ritchie (Bioinform., 2016)

Kbdock - Searching and Organising the Structural Space of Protein-Protein Interactions. - Marie-Dominique Devignes; Malika Smaïl-Tabbone; David W. Ritchie (ERCIM News, 2016)

Associating Gene Ontology Terms with Pfam Protein Domains. - Seyed Ziaeddin Alborzi; Marie-Dominique Devignes; David W. Ritchie (IWBBIO (2), 2017)

ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains. - Seyed Ziaeddin Alborzi; Marie-Dominique Devignes; David W. Ritchie (BMC Bioinform., 2017)

Neighborhood-Based Label Propagation in Large Protein Graphs. - Sabeur Aridhi; Seyed Ziaeddin Alborzi; Malika Smaïl-Tabbone; Marie-Dominique Devignes; David W. Ritchie (CoRR, 2017)

Exploiting Complex Protein Domain Networks for Protein Function Annotation. - Bishnu Sarker; David W. Ritchie; Sabeur Aridhi (COMPLEX NETWORKS (2), 2018)

Computational discovery of direct associations between GO terms and protein domains. - Seyed Ziaeddin Alborzi; David W. Ritchie; Marie-Dominique Devignes (BMC Bioinform., 2018)

Functional Annotation of Proteins using Domain Embedding based Sequence Classification. - Bishnu Sarker; David W. Ritchie; Sabeur Aridhi (KDIR, 2019)

EROS-DOCK: protein-protein docking using exhaustive branch-and-bound rotational search. - Maria Elisa Ruiz Echartea; Isaure Chauvot de Beauchêne; David W. Ritchie (Bioinform., 2019)

GrAPFI: predicting enzymatic function of proteins from domain similarity graphs. - Bishnu Sarker; David W. Ritchie; Sabeur Aridhi (BMC Bioinform., 2020)

PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions. - Seyed Ziaeddin Alborzi; Amina Ahmed Nacer; Hiba Najjar; David W. Ritchie; Marie-Dominique Devignes (PLoS Comput. Biol., 2021)