INRIA Nancy INRIA Nancy

      Dave Ritchie

      Full List of Publications, Presentations and Posters

      Publications

       View them on Google Scholar.

      2019
      • EROS-DOCK: Protein-Protein Docking Using Exhaustive Branch-and-Bound Rotational Search. ME Echartea Ruiz, I Chauvot de Beauchêne, DW Ritchie (2019). Bioinformatics.
      • Characterization of a relaxase belonging to the MOBT family, a widespread family in Firmicutes mediating the transfer of ICEs. N Soler, E Roberts, I Chauvot de Beauchêne, P Monteiro, V Libante, B Maigret, J Staub, DW Ritchie, G Guédon, S Payot, MD Devignes, N Leblond-Bourget (2019). Mobile DNA. Mobile DNA, 10, 18.
      • Exploiting Complex Protein Domain Networks for Protein Function Annotation. B Sarker, DW Ritchie, S Aridhi (2019). In: L Aiello, C Cherifi, H Cherifi, R Lambiotte, P Lió, L Rocha (eds). Complex Networks and Their Applications VII. COMPLEX NETWORKS 2018. Studies in Computational Intelligence, vol 813., Springer, Cham. 598-610.
      2018
      • The CYP71AZ P450 Subfamily: A Driving Factor for the Diversification of Coumarin Biosynthesis in Apiaceous Plants. C Kreiger, S Roselli, S Kellner-Thielmann, G Galati, B Schneider, J Grosjean, A Olry, DW Ritchie, U Matern, F Bourgaud, A Hehn (2018). Frontiers in Plant Science, 9, 820.
      • Computational Discovery of Direct Associations between GO terms and Protein Domains. SZ Alborzi, DW Ritchie, M-D Devignes (2018). BMC Bioinformatics, 19(Suppl 14), 213.
      • PDB-wide identification of biological assemblies from conserved quaternary structure geometry. S Dey, DW Ritchie, ED Levy (2018). Nature Methods, 15, 67-72.
      2017
      • Associating Gene Ontology Terms with Pfam Domains. SZ Alborzi, M-D Devignes, DW Ritchie (2017). LNCS 10209, 127-138 (IWBBIO 2017).
      • ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains. SZ Alborzi, M-D Devignes, DW Ritchie (2017). BMC Bioinformatics, 18, 107.
      • A bacterial artificial chromosome (BAC) genomic approach reveals partial clustering of the furanocoumarin pathway genes in parsnip. S. Roselli, A. Olry, S. Vautrin, O. Coriton, D.W. Ritchie, G. Galati, N. Navrot, C. Krieger, G. Vialart, H. Bergès, F. , Bourgaud, A. Hehn (2017). The Plant Journal, 89, 1119-1132.
      2016
      • Modeling and Minimising CAPRI Round 30 Symmetrical Protein Complexes from CASP-11 Structural Models. M. El Houasli, B. Maigret, M.-D. Devignes, A. W. Ghoorah, S. Grudinin, D.W. Ritchie (2016). Proteins, 84, 463-469.
      • PEPSI-Dock: a detailed data-driven protein-protein interaction potential accelerated by polar Fourier correlation. E. Neveu, D.W. Ritchie, P. Popov, and S. Grudinin (2016). Bioinformatics, 32, i693-i701 (ECCB 2016).
      • Protein-protein docking by fast generalized Fourier transforms on 5D rotational manifolds. D. Padhorny, A. Kazennov, B.S. Zerbe, K.A. Porter, B. Xia, S.E. Mottarella, Y. Kholodov, D.W. Ritchie, S. Vajda, and D. Kozakov (2016). PNAS, 113, E4286-E4273.
      • Calculating and scoring high quality multiple flexible protein structure alignments. D.W. Ritchie (2016). Bioinformatics, 32, 2650-2658.
      • Classification and Exploration of 3D Protein Domain Interactions Using Kbdock. A.W. Ghoorah, M.-D. Devignes, M. Smail-Tabbone, D.W. Ritchie (2016). in Methods in Molecular Biology 1415 - Data Mining Techniques for the Life Sciences (Eds. O. Carugo and F. Eisenhaber), 2, 91-105.
      • Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment. M. Lensink, ... D.W. Ritchie ... and many others (2016). Proteins, in press.
      • Spherical Polar Fourier Assembly of Protein Complexes with Arbitrary Point Group Symmetry. D.W. Ritchie and S. Grudinin (2016). Journal of Applied Crystallography, 49(1), 158-167. [PDF].
      2015
      • GESSE: Predicting Drug Side Effects from Drug-Target Relationships. V.I. Perez-Nueno, M. Souchet, A.S. Karaboga, D.W. Ritchie (2015). J. Chem. Inf. Model., 55, 1804-1823, and Front Cover Illustration.
      • EC-PSI: Associating Enzyme Commision Numbers with Pfam Domains. S.Z. Alborzi, M.-D. Devignes, D.W. Ritchie (2015). JOBIM 2015, to appear.
      • Unraveling the molecular architecture of a G protein-coupled receptor/β-arrestin/Erk module complex. T. Bourquard, F. Landomiel, E. Reiter, P. Crépieux, D.W. Ritchie, J. Azé, A. Poupon (2015). Scientific Reports, 5, 10760.
      • A Structure-Based Classification and Analysis of Protein Domain Family Binding Sites and Their Interactions. A.W. Ghoorah, M.-D. Devignes, S.Z. Alborzi, M. Smail-Tabbone, D.W. Ritchie, (2015). Biology, 4(2), 327-343.
      2014
      • GES polypharmacology fingerprints: A novel approach for drug repositioning. V.I. Perez-Nueno, A. Karaboga, M. Suchet, D.W. Ritchie, (2014). J. Chem. Inf. Model., 54, 720-734, and Front Cover Illustration.
      • KBDOCK 2013: A spatial classification of 3D protein domain family interactions. A.W. Ghoorah, M.-D. Devignes, M. Smail-Tabbone, D.W. Ritchie, (2014). Nucleic Acids Research, 42, D389-D395.
      2013
      • Protein Docking Using Case-Based Reasoning. A.W. Ghoorah, M. Smail-Tabbone, M.-D. Devignes, D.W. Ritchie, (2013). Proteins: Structure, Function, Bioinformatics, 81, 2150-2158.
      • Blind Prediction of Interfacial Water Positions in CAPRI. M. Lensink, S. Wodak, ... M. Chavent, D.W. Ritchie, ... (2013). Proteins: Structure, Function, Bioinformatics DOI: 10.1002/prot.24439.
      • gEMpicker: A Highly Parallel GPU-Accelerated Particle Picking Tool for Cryo-Electron Microscopy. T.V. Hoang, X. Cavin, P. Schultz, D.W. Ritchie, (2013). BMC Structural Biology, 2013, 13:25.
      • gEMfitter: A highly parallel FFT-based 3D density fitting tool with GPU texture memory acceleration. T.V. Hoang, X. Cavin, D.W. Ritchie, (2013). Journal of Structural Biology, Journal of Structural Biology. 184, 348-354.
      • Spherical Harmonic Molecular Surfaces (ParaSurf and ParaFit). D.W. Ritchie, V.I. Perez-Nueno (2013). In: Scaffold-Hopping in Medicinal Chemistry, editor: N. Brown, Wiley-VCH, pages 183-193.
      • Recent Trends and Future Prospects in Computational GPCR Drug Discovery: From Virtual Screening to Polypharmacology. A. Carrieri, V.I. Perez-Nueno, G. Lentini, D.W. Ritchie, V.I. Perez-Nueno (2013). Current Topics in Medicinal Chemistry, 13(9) 1069-1097.
      • DockTrina: Docking triangular protein trimers. P. Popov, D.W. Ritchie, S. Grudinin (2013). Proteins: Structure, Function, Bioinformatics, 82, 34-44.
      2012
      • Fast Protein Structure Alignment using Gaussian Overlap Scoring of Backbone Peptide Fragment Similarity. D.W. Ritchie, A.W. Ghoorah, L. Mavridis, V. Venkatraman (2012). Bioinformatics 28(24) 3274-3281. Supplementary Materials.
      • Flexible protein docking refinement using pose-dependent normal mode analysis. V. Venkatraman, D.W. Ritchie (2012). Proteins: Struct. Func. Bioinf. 80, 2262-2274.
      • Predicting Multi-component Protein Assemblies Using an Ant Colony Approach. V. Venkatraman, D.W. Ritchie (2012). International Journal of Swarm Intelligence Research, 3, 19-31.
      • Detecting Drug Promiscuity Using Gaussian Ensemble Screening. V.I. Pérez-Nueno, V. Venkatraman, L. Mavridis, D.W. Ritchie, (2012). J. Chem. Inf. Model. 52(8), 1948-1961.
      • Recent Trends and Applications in 3D Virtual Screening. L. Ghemtio, V.I. Pérez-Nueno, V. Leroux, Y. Asses, M. Souchet, L. Mavridis, B. Maigret, D.W. Ritchie, (2012). Combinatorial Chemistry & High Throughput Screening. 15(10), 749-769.
      • HIV-PDI: A Protein Drug Interaction Resource for Structural Analyses of HIV Drug Resistance: 2. Examples of Use and Proof-of-Concept. L. Ghemtio, M. Souchet, A. Djikeng, L. Keminse, P. Kelbert, D.W. Ritchie, B. Maigret, O. Ouwe-Missi-Oukem-Boyer. Journal of Health & Medical Informatics 2, 105 (2011).
      • 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]
      2011
      • 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.
      2010
      • 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.
      2009
      • 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.
      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. 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]
      2007
      • 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.
      2006
      • 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]
      2005
      • 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]
      2004
      • 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]
      2003
      • 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]
      2000 and earlier
      • 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]

      Summer Schools
      • Protein-Protein Docking -Current Methods and New Challenges, VII Escola de Modelagem Molecular em Sistemas Biologicos, LNCC, Petropolis, Brasil, 2014. [PDF]
      • Protein Docking and 3D Ligand-Based Virtual Screening, Lipari School on Bioinformatics and Computational Biology, Lipari, Italy, 2012. [SLIDES]
      • Protein Docking and Molecular Shape Recognition using Polar Fourier Correlations, 3rd Strasbourg Summer School on Chemoinformatics, Strasbourg, France, 2012. [PDF]
      • Using Graphics Processors to Accelerate Protein Docking Calculations, Programmation multicoeurs en bio-informatique, Lille, Lille, France, 2012. [PDF]

      Presentations

      A lot of the titles below look similar, but each talk is often slightly different. If you follow chronologically, I hope you will detect some kind of "progression".

      • Modeling Symmetrical Protein Structures in the CASP/CAPRI Docking Experiment, MIA Toulouse, 2017. [PDF]
      • Modeling Symmetrical Protein Complexes using SAM Soft Docking. 1st Meeting of the CPER "Innovations Technologiques et Modélisation pour la Médecine de Précision" (IT2MP), CHU Nancy, 2016. [PDF]
      • Modeling Symmetrical CASP/CAPRI Complexes using SAM, 6th CAPRI Evaluation Meeting, Tel Aviv, 2016. [PDF]
      • KBDOCK - A Case-Based Reasoning Approach to Model 3D Protein Complexes, Plateau de Modélisation Moléculaire Multi-échelle, Reims, 2015. [PDF]
      • Modeling Protein Docking using Polar Fourier Correlations and Case-Based Reasoning University of Oxford, 2014. [PDF]
      • Modeling Protein Docking using Polar Fourier Correlations and Case-Based Reasoning LGM, UPMC, Paris, 2013. [PDF]
      • Protein Docking and Molecular Shape recognition using Polar Fourier Correlations, LIMOS, Clermont-Ferrand, 2013. [PDF]
      • KBDOCK - A Case-Based Reasoning Approach to Model 3D Protein Complexes, LIMOS, Clermont-Ferrand, 2013. [PDF]
      • KBDOCK - A Case-Based Reasoning Approach to Model 3D Protein Complexes, Integrative Approaches for Modeling Biomolecular Complexes, Nice, 2013. [PDF]
      • KBDOCK - A Case-Based Reasoning Approach to Model 3D Protein Complexes, 5th CAPRI Evaluation Meeting, Utrecht, 2013. [PDF]
      • Protein Docking and Molecular Shape recognition using Polar Fourier Correlations, Structural Bioinformatics Group, Pasteur Institute, 2012. [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).

      Posters
      • Automatically Associating Enzyme EC Numbers with Pfam Protein Domains to Enrich Protein Structure Annotation. JOBIM-2015, Clermont-Ferrand, 2015.
      • Automatically Associating Enzyme EC Numbers with Pfam Protein Domains to Enrich Protein Structure Annotation. ISMB/ECCB-2015, Dublin, 2015.
      • A Detailed Data-Driven Protein-Protein Interaction Potential Accelerated By Polar Fourier Correlation GGMM-2015, Sète, 2015.
      • A Detailed Data-Driven Protein-Protein Interaction Potential Accelerated By Polar Fourier Correlations. BCBC-2015, Basel, 2015.
      • GESSE: Predicting Drug Side Effects from Drug-Target Relationships. IWBBIO-2015, Granada, 2015. [PDF]
      • Fine-Grained Structure-Function Classification of Pfam Protein Domain Families: A Case Study Using CYP450. ECCB'14, Strasbourg, 2014. [PDF]
      • A novel and powerful preclinical compound profiling and drug repositioning tool: GES polypharmacology fingerprints. 6th Journèes de la SFCi, Nancy, 2013.
      • GES polypharmacology fingerprints: a novel and powerful drug repositioning tool. 246th ACS National Meeting, Indianapolis, 2013.
      • Prediction of Complexes with Point Group Symmetry using Spherical Polar Fourier Docking Correlations. ISMB-3DSIG 2013, Berlin, 2013. [PDF]
      • A Comprehensive Comparison of Protein Structural Alignment Algorithms. ISMB-3DSIG 2012, Long Beach, California, 2012. [PDF]
      • 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

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