David W. Ritchie

Publication Activity (10 Years)

Years Active: 1997-2021
Publications (10 Years): 12

Top Topics

Label Propagation

Protein Interaction

Top Venues

J. Chem. Inf. Model.

Publications

Seyed Ziaeddin Alborzi, Amina Ahmed Nacer, Hiba Najjar, David W. Ritchie, Marie-Dominique Devignes
PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions. PLoS Comput. Biol. 17 (8) (2021)
Bishnu Sarker, David W. Ritchie, Sabeur Aridhi
GrAPFI: predicting enzymatic function of proteins from domain similarity graphs. BMC Bioinform. 21 (1) (2020)
Bishnu Sarker, David W. Ritchie, Sabeur Aridhi
Functional Annotation of Proteins using Domain Embedding based Sequence Classification. KDIR (2019)
Maria Elisa Ruiz Echartea, Isaure Chauvot de Beauchêne, David W. Ritchie
EROS-DOCK: protein-protein docking using exhaustive branch-and-bound rotational search. Bioinform. 35 (23) (2019)
Bishnu Sarker, David W. Ritchie, Sabeur Aridhi
Exploiting Complex Protein Domain Networks for Protein Function Annotation. COMPLEX NETWORKS (2) (2018)
Seyed Ziaeddin Alborzi, David W. Ritchie, Marie-Dominique Devignes
Computational discovery of direct associations between GO terms and protein domains. BMC Bioinform. (14) (2018)
Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, David W. Ritchie
ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains. BMC Bioinform. 18 (1) (2017)
Sabeur Aridhi, Seyed Ziaeddin Alborzi, Malika Smaïl-Tabbone, Marie-Dominique Devignes, David W. Ritchie
Neighborhood-Based Label Propagation in Large Protein Graphs. CoRR (2017)
Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, David W. Ritchie
Associating Gene Ontology Terms with Pfam Protein Domains. IWBBIO (2) (2017)
Émilie Neveu, David W. Ritchie, Petr Popov, Sergei Grudinin
PEPSI-Dock: a detailed data-driven protein-protein interaction potential accelerated by polar Fourier correlation. Bioinform. 32 (17) (2016)
Marie-Dominique Devignes, Malika Smaïl-Tabbone, David W. Ritchie
Kbdock - Searching and Organising the Structural Space of Protein-Protein Interactions. ERCIM News 2016 (104) (2016)
David W. Ritchie
Calculating and scoring high quality multiple flexible protein structure alignments. Bioinform. 32 (17) (2016)
Violeta I. Pérez-Nueno, Michel Souchet, Arnaud Sinan Karaboga, David W. Ritchie
GESSE: Predicting Drug Side Effects from Drug-Target Relationships. J. Chem. Inf. Model. 55 (9) (2015)
Anisah W. Ghoorah, Marie-Dominique Devignes, Malika Smaïl-Tabbone, David W. Ritchie
KBDOCK 2013: a spatial classification of 3D protein domain family interactions. Nucleic Acids Res. 42 (Database-Issue) (2014)
Violeta I. Pérez-Nueno, Arnaud Sinan Karaboga, Michel Souchet, David W. Ritchie
GES Polypharmacology Fingerprints: A Novel Approach for Drug Repositioning. J. Chem. Inf. Model. 54 (3) (2014)
Violeta I. Pérez-Nueno, Vishwesh Venkatraman, Lazaros Mavridis, David W. Ritchie
Detecting Drug Promiscuity Using Gaussian Ensemble Screening. J. Chem. Inf. Model. 52 (8) (2012)
David W. Ritchie, Anisah W. Ghoorah, Lazaros Mavridis, Vishwesh Venkatraman
Fast protein structure alignment using Gaussian overlap scoring of backbone peptide fragment similarity. Bioinform. 28 (24) (2012)
Vishwesh Venkatraman, David W. Ritchie
Predicting Multi-Component Protein Assemblies Using an Ant Colony Approach. Int. J. Swarm Intell. Res. 3 (3) (2012)
Anisah W. Ghoorah, Marie-Dominique Devignes, Malika Smaïl-Tabbone, David W. Ritchie
Spatial clustering of protein binding sites for template based protein docking. Bioinform. 27 (20) (2011)
Violeta I. Pérez-Nueno, David W. Ritchie
Using Consensus-Shape Clustering To Identify Promiscuous Ligands and Protein Targets and To Choose the Right Query for Shape-Based Virtual Screening. J. Chem. Inf. Model. 51 (6) (2011)
Violeta I. Pérez-Nueno, Vishwesh Venkatraman, Lazaros Mavridis, David W. Ritchie
Predicting drug polypharmacology using a novel surface property similarity-based approach. J. Cheminformatics 3 (S-1) (2011)
Jérôme Azé, Thomas Bourquard, Sylvie Hamel, Anne Poupon, David W. Ritchie
Using Kendall-τ Meta-Bagging to Improve Protein-Protein Docking Predictions. PRIB (2011)
Vishwesh Venkatraman, Violeta I. Pérez-Nueno, Lazaros Mavridis, David W. Ritchie
Comprehensive Comparison of Ligand-Based Virtual Screening Tools Against the DUD Data set Reveals Limitations of Current 3D Methods. J. Chem. Inf. Model. 50 (12) (2010)
David W. Ritchie, Vishwesh Venkatraman, Lazaros Mavridis
Using Graphics Processors to Accelerate Protein Docking Calculations. HealthGrid (2010)
Lazaros Mavridis, David W. Ritchie
3D-Blast: 3D Protein Structure Alignment, Comparison, and Classification Using Spherical Polar Fourier Correlations. Pacific Symposium on Biocomputing (2010)
David W. Ritchie, Vishwesh Venkatraman
Ultra-fast FFT protein docking on graphics processors. Bioinform. 26 (19) (2010)
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, Petros Daras
SHREC'10 Track: Protein Model Classification. 3DOR@Eurographics (2010)
Gary Macindoe, Lazaros Mavridis, Vishwesh Venkatraman, Marie-Dominique Devignes, David W. Ritchie
HexServer: an FFT-based protein docking server powered by graphics processors. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Violeta I. Pérez-Nueno, Sofia Pettersson, David W. Ritchie, José I. Borrell, Jordi Teixidó
Discovery of Novel HIV Entry Inhibitors for the CXCR4 Receptor by Prospective Virtual Screening. J. Chem. Inf. Model. 49 (4) (2009)
Violeta I. Pérez-Nueno, David W. Ritchie, José I. Borrell, Jordi Teixidó
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. J. Chem. Inf. Model. 48 (11) (2008)
Violeta I. Pérez-Nueno, David W. Ritchie, Obdulia Rabal, Rosalia Pascual, José I. Borrell, Jordi Teixidó
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. J. Chem. Inf. Model. 48 (3) (2008)
David W. Ritchie, Dima Kozakov, Sandor Vajda
Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions. Bioinform. 24 (17) (2008)
Lazaros Mavridis, Brian D. Hudson, David W. Ritchie
Toward High Throughput 3D Virtual Screening Using Spherical Harmonic Surface Representations. J. Chem. Inf. Model. 47 (5) (2007)
Alessandra Fano, David W. Ritchie, Antonio Carrieri
Modeling the Structural Basis of Human CCR5 Chemokine Receptor Function: From Homology Model Building and Molecular Dynamics Validation to Agonist and Antagonist Docking. J. Chem. Inf. Model. 46 (3) (2006)
David W. Ritchie, Graham J. L. Kemp
Fast computation, rotation, and comparison of low resolution spherical harmonic molecular surfaces. J. Comput. Chem. 20 (4) (1999)
David W. Ritchie, Graham J. L. Kemp
Modeling Antibody Side Chain Conformations Using Heuristic Database Search. ISMB (1997)