Dave Ritchie

I am an INRIA Research Director at INRIA Nancy Grand-Est, which is one of the eight INRIA centres in France (INRIA YouTube). I am a member of the Orpailleur Team which is based in the LORIA. Some of my research is funded by the ANR. Together with Sergei Grudinin and Valentin Gordeliy, I am one of the partners in Project PEPSI. Previously, I was funded by a grant from the ANR Chaires d'Excellence programme.

• All of The Above - Dave Ritchie
• People Pictures

NEW PhD Opportunity: Multi-Component Protein-Protein Docking [PDF]

• This is a project proposed for competitive selection by the IAEM doctoral school. The successful candidate will be fully funded by the Université de Lorraine. To apply on-line, please use the above link. Please note, you must have or expect to have a Masters degree in a relevant subject as a minimum qualification for entry to this PhD program.

• Bursaries: Each year, INRIA funds a number of doctoral thesis and postdoc projects. These are awarded on a competitive basis. Please see: PhD positions and Postdoc vacancies. I will add some bioinformatics project proposals soon. In a similar manner, the IAEM doctoral school funds some doctoral theses in informatics. If you wish to discuss a possible IAEM thesis project, please contact me around November-January with a view to applying in February.
• Internships: Each year, INRIA supports a good number of internships (normally at masters-level) in collaboration with foreign universities. These opportunities are posted in the partner institutes in December. Please see: INRIA Internships.
• Enquiries: I am always open to enquiries. For the best chance of success, you should have a good idea of what you would like to do and how you might get funding.

Hex Protein Docking program for Windows-XP + Mac OS X + Linux (all with GPU acceleration)

Hex Server - run Hex on our GPU-powered server

KBDOCK Knowledge-Based Docking - a database of 3D protein interactions and binding sites

3D-Blast Protein Fold Recognition - a server for sequence-independent 3D protein shape comparison and alignment

• Université de Lorraine - Faculté des Sciences et Technologies
• Informatics Masters - Nancy Université
• Systems Biology Masters - Université de la Grande Région and Integrative Biology at Nancy Université
• Bioinformatique en Lorraine
• MBI (Modeling Biomolecules and their Interactions)
• Talc cluster
• SFBI (French Bioinformatics Society)
• ReNaBI (French National Bioinformatics Platforms Network)
• SFCi (French Chemoinformatics Society)
• GdR Bionfiormatique Moléculaire (Groupement de Recherche)
• MAEM (Maturation of RNA and Molecular Enzymes)
• EDAM (Equipe de Dynamique des Assemblages Membranaires)
• CMT (Chimie et Biochimie Theéoriques)
• Definition of Bioinformatics (and why biology needs computing)
• "Ten Simple Rules" Collection (local copy)
• LORIA WIKI
• Ecole Doctorale IAEM Lorraine and Départment de Formation Doctoral (DFD) Informatique
• Nancy Université and Université de Lorraine
• International Grants

• Modeling Protein-Protein Interactions by Rigid-Body Docking. D.W. Ritchie (2012) in Drug Design Strategies: Computational Techniques and Applications, pp 56-86 (editors T. Clark and L. Banting). RSC Publishing, Cambridge, UK. ISBN 978-1-84973-167-6.
• Exploring c-met kinase flexibility by sampling and clustering its conformational space. Y. Asses, V. Venkatraman, V. Leroux, D.W. Ritchie, B. Maigret (2012). Proteins: Struct. Func. Bioinf. 80(4), 1227-1238.
• Representing and comparing protein folds and fold families using 3D shape-density representations. L. Mavridis, A.W. Ghoorah, V. Venkatraman, D.W. Ritchie (2012). Proteins: Struct. Func. Bioinf. 80(2), 530-545. [PDF]

• Identifying and characterizing promiscuous targets: Implications for virtual screening. V.I. Pérez-Nueno, D.W. Ritchie (2011). Expert Opinion On Drug Discovery, 7(1), 1-17.
• Spatial clustering of protein binding sites for template based protein docking. A. Ghoorah, M.-D. Devignes, M. Smail-Tabbone, D.W. Ritchie (2011). Bioinformatics, 27, 2820-2827, [PDF] (see Supplementary Materials for detailed homology docking results).
• Predicting drug promiscuity using spherical harmonic (SH) shape-based similarity comparisons. V.I. Pérez-Nueno, V. Venkatraman, L. Mavridis, D.W. Ritchie (2011). The Open Conference Proceedings Journal, 2, 113-129.
• Using Kendall-τ meta-bagging to improve protein-protein docking predictions. J. Azé, T. Bourquard, S. Hamel, A. Poupon, D.W. Ritchie (2011). Pattern Recognition in Bioinformatics (PRIB 2011) 284-295.
• Predicting Multicomponent Protein Assemblies Using an Ant Colony Approach V. Venkatraman, D.W. Ritchie (2011). International Conference on Swarm Intelligence (ICSI 2011). [PDF]
• Protein-protein docking based on shape complementarity and Voronoi fingerprint. T. Bourquard, J. Azé, A. Poupon, D.W. Ritchie (2011). Journées Ouvertes Biologie Informatique et Mathématiques (JOBIM) 2011, pp 9-16 (in French). [PDF]
• Using Consensus-Shape Clustering To Identify Promiscuous Ligands and Protein Targets and To Choose the Right Query for Shape-Based Virtual Screening. V.I. Pérez-Nueno, D.W. Ritchie (2011). J. Chem. Inf. Model. 51(6) 1233-1248.
• Applying in silico Tools to the Discovery of Novel CXCR4 Inhibitors. V.I. Pérez-Nueno, D.W. Ritchie (2011). Drug Discovery Development Research. 72, 95-111.
• Using spherical harmonic surface property representations for ligand-based virtual screening. V.I. Pérez-Nueno, V. Venkatraman, L. Mavridis, T. Clark, D.W. Ritchie (2011). Molecular Informatics. 30, 151-159.

• A Comprehensive Comparison of Ligand-Based Virtual Screening Tools Against the DUD Dataset Reveals Limitations of Current 3D Methods. V. Venkatraman, V.I. Pérez-Nueno, L. Mavridis, D.W. Ritchie (2010). J. Chem. Inf. Model. 50, 2079-2093. [PDF]
• Using Graphics Processors to Accelerate Protein Docking Calculations. D.W. Ritchie, V. Venkatraman and L. Mavridis (2010). Healthgrid Applications and Core Technologies - Proceedings of HealthGrid 2010, pp 146-155. [PDF]
• Ultra-Fast FFT Protein Docking On Graphics Processors. D.W. Ritchie, V. Venkatraman (2010). Bioinformatics, 26, 2398-2405 (see supplementary results for detailed CPU/GPU precision differences).
• HexServer: an FFT-based protein docking server powered by graphics processors. G. Macindoe, L. Mavridis, V. Venkatraman, M.-D. Devignes, D.W. Ritchie (2010). Nucleic Acids Research, 38, W445-W449.
• SHREC-10 Track: Protein Models. L. Mavridis, V. Venkatraman, D. W. Ritchie, N. Morikawa, R. Andonov, A. Cornu, N. Malod-Dognin, J. Nicolas, M. Temerinac-Ott, M. Reisert, H. Burkhardt, A. Axenopoulos, 3DOR: Eurographics Workshop on 3D Object Retrieval (2010), 117-124. [PDF]
• 3D-Blast: 3D Protein Structure Alignment, Comparison, and Classification Using Spherical Polar Fourier Correlations. L. Mavridis, D.W. Ritchie (2010). Pacific Symposium on Biocomputing 15 281-292.

• Identification and characterisation of a novel immune-type receptor (NITR) gene cluster in the European sea bass, Dicentrarchus labrax, reveals recurrent gene expansion and diversification by positive selection. S. Ferraresso, H. Kuhl, M. Milan, D.W. Ritchie, C.J. Secombes, R. Reinhardt, L. Bargelloni (2009). Immunogenetics 61 773-788.
• Biological profiling of anti-HIV agents and insights into CCR5 antagonist binding using in silico techniques. A. Carrieri, V.I. Perez-Nueno, A. Fano, C. Pistone, D.W. Ritchie, and J. Teixido (2009). ChemMedChem 4(7) 1153-1163.
• Discovery of Novel HIV Entry Inhibitors for the CXCR4 Receptor by Prospective Virtual Screening. V.I. Perez-Nueno, S. Pettersson, D.W. Ritchie, J. I. Borrell, and J. Teixido (2009). J. Chem. Inf. Model. 49(4) 810-823.

• 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. V.I. Perez-Nueno, D.W. Ritchie, J. I. Borrell, and J. Teixido (2008). J. Chem. Inf. Model. 48(11) 2146-2165.
• Accelerating and Focusing Protein-Protein Docking Correlations Using Multi-Dimensional Rotational FFT Generating Functions. D.W. Ritchie, D. Kozakov, and S. Vajda (2008). Bioinformatics. 24 1865-1873.
• 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. V.I. Perez-Nueno, D.W. Ritchie, O. Rabal, R. Pascual, J.I. Borrell, and J. Teixido (2008). J. Chem. Inf. Model. 48(3) 509-533. and Front Cover Illustration.
• Recent progress and future directions in protein-protein docking D.W. Ritchie (2008). Curr. Prot. Pep. Sci. 9(1), 1-15. [PDF]

• Toward high throughput 3D virtual screening using spherical harmonic molecular surface representations. L. Mavridis, B.D. Hudson, and D.W. Ritchie (2007). J. Chem. Inf. Model. 47(5), 1787-1796.

• A Non-Atom-Based Paradigm for Modeling, QSAR and QSPR, T. Clark, M. Ford, J. Essex, W.G. Richards and D.W. Ritchie (2006). EuroQSAR 2004 Proceedings, E. Aki and I. Yalcin (Eds), Computer Aided Drug Design and Development Society in Turkey, Ankara, pp 536-7.
• Modelling the structural basis of human CCR5 chemokine receptor function: from homology model-building and molecular dynamics validation to agonist and antagonist docking, A. Fano, D.W. Ritchie, A. Carrieri (2006) J. Chem. Inf. Model., 46(3), 1223-1235. [PDF]

• High Order Analytic Translation Matrix Elements For Real Space Six-Dimensional Polar Fourier Correlations, D.W. Ritchie (2005) J. Appl. Cryst. 38, 808-818 . [PDF]
• Docking Essential Dynamics Eigenstructures, D. Mustard and D.W. Ritchie (2005) PROTEINS: Struct. Funct. Bioinf. 60(2) 269-274. [PDF]

• Analysis of fish IL-1b and derived peptide sequences indicates conserved structures with species-specific IL-1 receptor binding: Implications for pharmacological design, A.I. Koussounadis, D.W. Ritchie, G.J.L. Kemp, C.J. Secombes (2004), Current Pharmaceutical Design, 10(31) 3857-3871. [PDF]
• Modelling Beta-Trefoil Proteins Using an Object-Oriented Database, A. Koussounadis, D.W. Ritchie, C.J. Secombes (2004). In: 21st Annual British National Conference on Databases (BNCOD21) Volume 2, pp59-67, Riccarton, Edinburgh: Heriot-Watt University. ISBN 1-904410-12-X. [PDF]

• Evaluation of Protein Docking Predictions Using Hex 3.1 in CAPRI Rounds 1 and 2, D.W. Ritchie (2003) PROTEINS: Struct. Funct. Genet. 52(1), 98-106. [PDF]

• Protein Docking Using Spherical Polar Fourier Correlations, D.W. Ritchie, G.J.L. Kemp (2000) PROTEINS: Struct. Funct. Genet. 39, 178-194. [PDF]
• Terminating eukaryote translation: domain 1 of release factor eRF1 functions in stop codon recognition, G. Bertram, H.A. Bell, D.W. Ritchie, G. Fullerton & I. Stansfield (2000), RNA 6(9), 1236-1247.
• Fast Computation, Rotation, and Comparison of Low Resolution Spherical Harmonic Molecular Surfaces, D.W. Ritchie, G.J.L. Kemp (1999) J. Comp. Chem. 20(4), 383-395. [PDF]
• Parametric Protein Shape Recognition, PhD Thesis, D.W. Ritchie, Departments of Computing Science and Molecular and Cell Biology, University of Aberdeen (1999). [PDF]
• Modeling Antibody Side Chain Conformations Using Heuristic Database Search, D.W. Ritchie, G.J.L. Kemp (1997), Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology (ISMB-97), pp237-240, AAAI Press, ISBN 1-57735-022-7.
• Using an Object-Oriented Database to Model Antibody Fv Fragments, D.W. Ritchie, Technical Report AUCS/TR9702 (1997), University of Aberdeen. [PDF]
• Expert Antibody Side Chain Placement, MSc Thesis, D.W. Ritchie, Department of Computing Science, University of Aberdeen (1995). [PDF]

• French: Algorithmes Haute-Performance pour la Reconnaissance de Formes Moléculaires [PDF]
• English: High Performance Algorithms for Molecular Shape Recognition [PDF]
• Collected papers 1999-2010 [PDF]

• Protein Docking and Molecular Shape recognition using Polar Fourier Correlations, GGMM_2011, La Rochelle, 2011. [PDF]
• Protein Docking and Molecular Shape recognition using Polar Fourier Correlations, Université de Reims Champagne-Ardennes, 2011. [PDF]
• Protein Docking and Molecular Shape recognition using Polar Fourier Correlations, Infochimie lab, Strasbourg, 2011. [PDF]
• Using Graphics Processors to Accelerate Protein Docking Calculations, LIX Bioinformatics Colloquium, Ecole Polytechnique, 2010. [PDF]
• Protein Docking and Molecular Shape recognition using Polar Fourier Correlations, GICC Tours, 2010. [PDF]
• Using Graphics Processors to Accelerate Protein Docking Calculations, HealthGrid 2010. [PDF]
• Protein Docking and Molecular Shape recognition using Polar Fourier Correlations, Fédération Charles Hermite, 2010. [PDF]
• ParaFit - Clustering and Classifying HIV Entry Inhibitors, Cepos Symposium 2010. [PDF]
• Using Spherical Harmonic Virtual Screening Tools to Compare and Classify HIV Entry Inhibitors for the CXCR4 and CCR5 Co-Receptors, Modeling-09, CCC Erlangen, 2009. [PDF]
• Protein Docking and Molecular Shape Recognition Using Polar Fourier Correlations, INRIA Grenoble - Rhone-Alpes, 2009. [PDF]
• Protein Docking and Molecular Shape Recognition Using Polar Fourier Correlations, Max Planck Institut Informatik, Saarbruecken, 2008. [PDF]
• Protein Docking - Predicting Protein-Protein Interactions at the Molecular Level, Scottish Bioinformatics Forum, Dundee, 2007. [PDF]
• Protein Docking and Molecular Shape Recognition Using Polar Fourier Correlations, LORIA, Vandouvres-les-Nancy, France, 2007. [PDF]
• Practical 5D FFT Docking, Modeling of Protein Interactions (MPI-2007), Lawrence, Kansas, 2007. [PDF]
• Structural Systems Biology - Computer Modeling of Protein-Protein Interactions, Aberdeen Systems Biology Symposium, 2007. [PDF]
• Protein Docking and Molecular Shape Recognition, John Innes Centre, Norwich 2006. [PDF]
• ParaFit-07, Various. [PDF]
• Protein Docking and Molecular Shape Recognition, UK QSAR Society Spring Meeting, Accelrys, 2006. [PDF]
• Protein Docking and Molecular Shape Recognition, Aberdeen Systems Biology Workshop, 2005. [PDF]
• Docking The CAPRI Rounds 3-5 Targets Using Essential Dynamics Eigenstructures, Gaeta, Italy 2004. [PDF]
• Hex Docking & CAPRI Results, CCC, Erlangen 2004; CMD, Portsmouth 2004. [PDF]
• Molecular Shape Recognition, Cresset BMD 2004. [PDF]
• Structure-Based Modelling of Protein-Protein Interactions, Bioinformatics Research Centre, Glasgow, 2003. [PDF]
• Seminar on Protein Docking, Chalmers University, Gothenburg, Sweden 2003. [PDF]
• Lecture on Protein Docking, Chalmers University, Gothenburg, Sweden 2003. [PDF]
• Overview of CAPRI, Scottish Protein Group, Dundee, Scotland 2002. [PDF]
• Evaluation of Hex in CAPRI, La Londe, France 2002. [PDF]
• Presentation Abstract: CNRS, Marseille, 2000.
• Presentation Abstract: Biomedical & Life Sciences, Glasgow 2000.
• Presentation Abstract: Chemistry Dept, Aberdeen 2000.
• Presentation Abstract: Model(l)ing '97, Erlangen (MGMS/WATOC).

• Representing and Comparing Protein Folds and Fold Families Using 3D Shape-Density Representations. ISMB-3DSIG 2011, Vienna, 2011. [PDF]
• A Comparison of Normal Mode Analysis Approaches for Modelling Flexibility in Protein-Protein Docking. ISMB-3DSIG 2011, Vienna, 2011. [PDF]
• Using Graphics Processors to Accelerate Protein Docking Calculations. GGMM_2011, La Rochelle, 2011. [PDF]
• Identifying promiscuous drugs and protein targets using spherical harmonic shape-based similarity comparisons, ICDDT, Dubai, 2011. [PDF]
• Using Voronoi fingerprints to re-score Hex protein-protein docking models, LIX Bioinformatics Colloquium, Ecole Polytechnique, 2010. [PDF]
• Extracting and visualising protein-protein complexes for knowledge-based docking, ECCB10, Ghent, 2010. [PDF]
• Using novel spherical harmonic consensus surface property representations to help choose the "right" query for "difficult" ligand-based virtual screening targets, EuroQSAR 2010, Rhodes, 2010. [PDF]
• Improving Rigid Body Protein-Protein Docking Using Fine-Grained Normal Mode Analysis, 3DSIG 2010, Boston, 2010. [PDF]
• A Novel 3D Shape-Based Indexing Scheme for the CATH Protein Structure Classification, 3DSIG 2010, Boston, 2010. [PDF]
• A Comphrehensive Comparison of Ligand-Based Virtual Screening Methods Against the DUD Dataset, 5th Joint Sheffield Conference on Chemoinformatics, Sheffield, 2010. [PDF]
• Fast FFT Protein-Protein Docking on Graphics Processors, 4th CAPRI Evaluation Meeting, Barcelona, 2009. [PDF]
• Developing a Knowledge-Based Approach to Protein-Protein Docking, 4th CAPRI Evaluation Meeting, Barcelona, 2009. [PDF]
• Using Human Expertise in Protein-Protein Docking: From Biological Knowledge to Interactive Simulations, 4th CAPRI Evaluation Meeting, Barcelona, 2009. [PDF]
• 3D-BLAST: Fast 3D Protein Shape Superposition, Comparision, and Classification, 3DSIG 2009: Structural Bioinformatics and Computational Biophysics, Stockholm, 2009. [PDF]
• MD Simulations in Explicit Solvent Can Improve Rigid Body Docking: A Case Study Using CAPRI Target 34, Flexibilité et Reconnaissance Biologique : de la biophysique aux modèles de donné INRIA, Sophia-Antipolis, March 2009. [PDF]
• Spherical harmonic molecular surface fragment matching for high throughput virtual drug screening, Targeting and Tinkering with Interaction Networks, IRB Barcelona, April 2008. [PDF]
• Analysis of ligand based shape matching and structure based docking methods for identifying HIV entry inhibitors for the CXCR4 and CCR5 receptors, Targeting and Tinkering with Interaction Networks, IRB Barcelona, 2008. [PDF]
• Comparison of ligand based shape matching and structure based docking methods for identifying HIV entry inhibitors for the CXCR4 and CCR5 receptors, 4th Joint Sheffield Conference on Chemoinformatics, 2007. [PDF]
• Towards High Throughput 3D Virtual Screening Using Spherical Harmonic Molecular Shape Representations, 4th Joint Sheffield Conference on Chemoinformatics, 2007. [PDF]
• Representing and Comparing Molecules Using Spherical Harmonic Expansions, 16th European Symposium on Quantitative Structure-Activity Relationships & Molecular Modelling, September 2006. [PDF]
• Representing and Comparing Molecules Using Spherical Harmonic Expansions, UK QSAR Society 2006 Spring Meeting. [PDF]
• A New Chemoinformatics-Based Approach to Protein Docking: Fourier Correlation of PCA-Selected Probe Potentials, Modeling of Protein Interactions in Genomes, Stony Brook, 2003. [PDF]
• Analysis of Fish IL-1B Indicates Conserved Structures and Species-Specific Interleukin-1 Receptor Binding, Aberdeen, 2003.
• Poster Abstract: Structural Genomics, Cambridge 2000
• Poster Abstract: GPC-VI, Chester 2000
• Poster Abstract: Frontiers in Visualisation '97, EBI, Cambridge
• Poster Abstract: MGMS Manchester 1997

My molecular shape-matching program "ParaFit" is marketed by Cepos InSilico.

Outside of work, my main activity is hiking. For me, it's a great way to relax and keep fit at the same time. When I lived in Scotland, I liked to go hiking in the Scottish highlands, mainly in the Cairngorms. Now, I very much like Les Vosges.

• Hiking Pictures

• Powering the Cell: Mitochondria by Harvard BioVisions and XVIVO
• An Inconvenient Truth by Al Gore

• LORIA Guide for Foreigners (mostly in English)
• AngloInfo (in English)
• AngloInfo Taxation (in English)
• impots.gouv.fr (in French)
• FrenchEntree.com (in English)
• Academic Careers Info (in English)

INRIA Nancy Grand Est
LORIA, Batiment B, Bureau B166
615 Avenue du Jardin Botanique
Campus Scientifique, BP239
54506 Vandoeuvre-les-Nancy, France
Phone : +33 3 83 59 30 45
E-mail: dave.ritchie AT loria.fr (please make your own AT sign)