Dave Ritchie

I moved to the LORIA on 1st January 2009 to work on the above project (HPASSB) within the Orpailleur Team. I am currently funded by the ANR as an INRIA Researcher Director, having been awarded a grant under the ANR Chaires d'Excellence 2008 programme. The LORIA is the home of INRIA Nancy Grand-Est, which is one of the eight main regional INRIA centres in France. I used to work as a lecturer at the University of Aberdeen. Here is my old Aberdeen Home Page.

• Stagieres: There are currently possibilties for one or more stagieres to work on projects relating to protein interactions.

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

On-line Hex Server

View the Docking Movie (best 100 antibody/lysozyme orientations).

• Bioinformatique en Lorraine
• MBI (Modeling Biomolecules and their Interactions)
• CCT G-BioModeL (Genomic and Biomolecular Modelling in Lorraine)
• MAEM (Maturation of RNA and Molecular Enzymes)
• VSM-G (Virtual Screening Manager for Grids)
• Definition of Bioinformatics (and why biology needs computing)
• LORIA WIKI
• International Grants
• Multi-Core Cluster Computing

• 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.
• 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.
• High Order Analytic Translation Matrix Elements For Real Space Six-Dimensional Polar Fourier Correlations, D.W. Ritchie (2005) J. Appl. Cryst. 38, 808-818 .
• Docking Essential Dynamics Eigenstructures, D. Mustard and D.W. Ritchie (2005) PROTEINS: Struct. Funct. Bioinf. 60(2) 269-274.
• 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.
• 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.
• 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.
• Protein Docking Using Spherical Polar Fourier Correlations, D.W. Ritchie & G.J.L. Kemp (2000) PROTEINS: Struct. Funct. Genet. 39, 178-194.
• 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.
• Parametric Protein Shape Recognition, PhD Thesis, D.W. Ritchie, Departments of Computing Science and Molecular and Cell Biology, University of Aberdeen (1998).
• 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
• Expert Antibody Side Chain Placement, MSc Thesis, D.W. Ritchie, Department of Computing Science, University of Aberdeen (1995).

• ParaFit - Clustering and Classifying HIV Entry Inhibitors, Cepos Symposium 2010.
• 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
• Protein Docking and Molecular Shape Recognition Using Polar Fourier Correlations, INRIA Grenoble - Rhone-Alpes, 2009
• Protein Docking and Molecular Shape Recognition Using Polar Fourier Correlations, Max Planck Institut Informatik, Saarbruecken, 2008
• Protein Docking - Predicting Protein-Protein Interactions at the Molecular Level, Scottish Bioinformatics Forum, Dundee, 2007
• Protein Docking and Molecular Shape Recognition Using Polar Fourier Correlations, LORIA, Vandouvres-les-Nancy, France, 2007
• Practical 5D FFT Docking, Modeling of Protein Interactions (MPI-2007), Lawrence, Kansas, 2007
• Structural Systems Biology - Computer Modeling of Protein-Protein Interactions, Aberdeen Systems Biology Symposium, 2007
• Protein Docking and Molecular Shape Recognition, John Innes Centre, Norwich 2006
• ParaFit-07
• Protein Docking and Molecular Shape Recognition, UK QSAR Society Spring Meeting, Accelrys, 2006
• Protein Docking and Molecular Shape Recognition, Aberdeen Systems Biology Workshop, 2005
• Docking The CAPRI Rounds 3-5 Targets Using Essential Dynamics Eigenstructures, Gaeta, Italy 2004
• Hex Docking & CAPRI Results, CCC, Erlangen 2004; CMD, Portsmouth 2004
• Molecular Shape Recognition, Cresset BMD 2004
• Structure-Based Modelling of Protein-Protein Interactions, Bioinformatics Research Centre, Glasgow (DTI/EPSRC Outreach) 2003
• Seminar on Protein Docking Chalmers University, Gothenburg, Sweden 2003
• Lecture on Protein Docking Chalmers University, Gothenburg, Sweden 2003
• Overview of CAPRI, Scottish Protein Group, Dundee, Scotland 2002
• Evaluation of Hex in CAPRI, La Londe, France 2002
• 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)

• Fast FFT Protein-Protein Docking on Graphics Processors, 4th CAPRI Evaluation Meeting, Barcelona, 2009.
• Developing a Knowledge-Based Approach to Protein-Protein Docking, 4th CAPRI Evaluation Meeting, Barcelona, 2009.
• Using Human Expertise in Protein-Protein Docking: From Biological Knowledge to Interactive Simulations, 4th CAPRI Evaluation Meeting, Barcelona, 2009.
• 3D-BLAST: Fast 3D Protein Shape Superposition, Comparision, and Classification, 3DSIG 2009: Structural Bioinformatics and Computational Biophysics, Stockholm, 2009.
• 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.
• Spherical harmonic molecular surface fragment matching for high throughput virtual drug screening, Targeting and Tinkering with Interaction Networks, IRB Barcelona, April 2008.
• 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, April 2008.
• 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, June 2007.
• Towards High Throughput 3D Virtual Screening Using Spherical Harmonic Molecular Shape Representations, 4th Joint Sheffield Conference on Chemoinformatics, June 2007.
• Representing and Comparing Molecules Using Spherical Harmonic Expansions, 16th European Symposium on Quantitative Structure-Activity Relationships & Molecular Modelling, September 2006.
• Representing and Comparing Molecules Using Spherical Harmonic Expansions, UK QSAR Society 2006 Spring Meeting.
• A New Chemoinformatics-Based Approach to Protein Docking: Fourier Correlation of PCA-Selected Probe Potentials, Modeling of Protein Interactions in Genomes, Stony Brook, 2003.
• 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.

I like to keep fit by hiking in the Scottish highlands, mainly in the Cairngorms. Since moving to France, I have started to discover Les Vosges.

• Various Pictures

• LORIA Guide for Foreigners
• AngloInfo (In English)
• AngloInfo Taxation (In English)
• impots.gouv.fr (In French)
• FrenchEntree.com (In English)

LORIA, INRIA Nancy Grand Est
Batiment B, Bureau B166
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)