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ORCIDDavid W. Ritchie
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2020 – today
- 2021
[j26]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)- 2020
- [j25]Bishnu Sarker, David W. Ritchie, Sabeur Aridhi:
GrAPFI: predicting enzymatic function of proteins from domain similarity graphs. BMC Bioinform. 21(1): 168 (2020)
2010 – 2019
- 2019
- [j24]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): 5003-5010 (2019) - [c8]Bishnu Sarker, David W. Ritchie, Sabeur Aridhi:
Functional Annotation of Proteins using Domain Embedding based Sequence Classification. KDIR 2019: 163-170 - 2018
- [j23]Seyed Ziaeddin Alborzi, David W. Ritchie, Marie-Dominique Devignes:
Computational discovery of direct associations between GO terms and protein domains. BMC Bioinform. 19-S(14): 53-66 (2018) - [c7]Bishnu Sarker, David W. Ritchie, Sabeur Aridhi:
Exploiting Complex Protein Domain Networks for Protein Function Annotation. COMPLEX NETWORKS (2) 2018: 598-610 - 2017
- [j22]Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, David W. Ritchie:
ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains. BMC Bioinform. 18(1): 107:1-107:11 (2017) - [c6]Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, David W. Ritchie:
Associating Gene Ontology Terms with Pfam Protein Domains. IWBBIO (2) 2017: 127-138 - [i2]Sabeur Aridhi, Seyed Ziaeddin Alborzi, Malika Smaïl-Tabbone, Marie-Dominique Devignes, David W. Ritchie:
Neighborhood-Based Label Propagation in Large Protein Graphs. CoRR abs/1708.07074 (2017) - 2016
- [j21]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): 693-701 (2016) - [j20]David W. Ritchie:
Calculating and scoring high quality multiple flexible protein structure alignments. Bioinform. 32(17): 2650-2658 (2016) - [i1]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) - 2015
- [j19]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): 1804-1823 (2015) - 2014
- [j18]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): 720-734 (2014) - [j17]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): 389-395 (2014) - 2012
- [j16]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): 3274-3281 (2012) - [j15]Vishwesh Venkatraman, David W. Ritchie:
Predicting Multi-Component Protein Assemblies Using an Ant Colony Approach. Int. J. Swarm Intell. Res. 3(3): 19-31 (2012) - [j14]Violeta I. Pérez-Nueno, Vishwesh Venkatraman, Lazaros Mavridis, David W. Ritchie:
Detecting Drug Promiscuity Using Gaussian Ensemble Screening. J. Chem. Inf. Model. 52(8): 1948-1961 (2012) - 2011
- [b1]David W. Ritchie:
Algorithmes Haute-Performance pour la Reconnaissance de Formes Moléculaires. (High Performance Algorithms for Molecular Shape Recognition). Henri Poincaré University, Nancy, France, 2011 - [j13]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): 2820-2827 (2011) - [j12]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): 19 (2011) - [j11]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): 1233-1248 (2011) - [c5]Jérôme Azé, Thomas Bourquard, Sylvie Hamel, Anne Poupon, David W. Ritchie:
Using Kendall-τ Meta-Bagging to Improve Protein-Protein Docking Predictions. PRIB 2011: 284-295 - 2010
- [j10]David W. Ritchie, Vishwesh Venkatraman:
Ultra-fast FFT protein docking on graphics processors. Bioinform. 26(19): 2398-2405 (2010) - [j9]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): 2079-2093 (2010) - [j8]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): 445-449 (2010) - [c4]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: 117-124 - [c3]David W. Ritchie, Vishwesh Venkatraman, Lazaros Mavridis:
Using Graphics Processors to Accelerate Protein Docking Calculations. HealthGrid 2010: 146-155 - [c2]Lazaros Mavridis, David W. Ritchie:
3D-Blast: 3D Protein Structure Alignment, Comparison, and Classification Using Spherical Polar Fourier Correlations. Pacific Symposium on Biocomputing 2010: 281-292
2000 – 2009
- 2009
- [j7]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): 810-823 (2009) - 2008
- [j6]David W. Ritchie, Dima Kozakov, Sandor Vajda:
Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions. Bioinform. 24(17): 1865-1873 (2008) - [j5]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): 509-533 (2008) - [j4]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): 2146-2165 (2008) - 2007
- [j3]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): 1787-1796 (2007) - 2006
- [j2]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): 1223-1235 (2006)
1990 – 1999
- 1999
- [j1]David W. Ritchie, Graham J. L. Kemp:
Fast computation, rotation, and comparison of low resolution spherical harmonic molecular surfaces. J. Comput. Chem. 20(4): 383-395 (1999) - 1997
- [c1]David W. Ritchie, Graham J. L. Kemp:
Modeling Antibody Side Chain Conformations Using Heuristic Database Search. ISMB 1997: 237-240
Coauthor Index
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