Dave Ritchie INRIA Nancy INRIA Nancy

      Dave Ritchie

      Computational Algorithms for Protein Structures and Interactions

      I am responsible for the Capsid research team at the LORIA / Inria Nancy research centre in Nancy, France. The team is common ("Equipe Projet Commun") to the CNRS, Inria, and the University of Lorraine.

      • Capsid Team web site

      • Team page (LORIA)
      • Team page (Inria)
      • LORIA Department 5


      People and Projects

      ANR Project PEPSI - with Sergei Grudinin

      Multi-component protein assembly using distance constraints - Maria Elisa Ruiz-Echartea

      Developing distributed graph-based approaches for large-scale protein function annotation and knowledge discovery - Bishnu Sarker



      Former Students and Postdocs

      Large-Scale Exploration of 3D Protein Domain Family Binding Sites - Zia Alborzi   [THESIS]

      Probability Theory Applied to Evolutionary Biology - Benoit Henry   [THESIS]

      3D Object Recognition Algorithms - Thai Van Hoang

      Protein Shape Analysis - Lazaros Mavridis

      Flexible Protein Docking - Vishwesh Venkatraman

      Re-Scoring Protein Docking Predictions - Thomas Bourquard

      Knowledge Discovery in Databases of Protein-Protein Interactions - Anisah Ghoorah   [THESIS]

      Developing Novel Virtual Screening Algorithms - Violeta Pérez-Nueno

      • People Pictures


      Vacancies/Opportunities

      I do not currently have funded vacancies, but please see below.

      • 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. In a similar manner, the IAEM doctoral school funds some doctoral theses in informatics.
        This year, we are proposing two PhD thesis projects (deadline 30/03/2017):
        • Protein function annotation (Big Data)
        • Flexible RNA-protein docking
      • 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.


      Software and Servers

      Hex Protein Docking program for Windows-XP + Mac OS X + Linux (all with GPU acceleration)
      Hex Server - run Hex on our GPU-powered server
      Sam - symmetry assembler program for protein complexes with arbitrary point group symmetry
      CGC - Clebsch-Gordan coefficient calculator- new!
      Kpax - protein structure alignment - version 5 now available! - for pair-wise and multiple alignments with or without flexibility

      GrAPFI - new! - protein sequence to EC number annotation by graph label propagation

      ECDomainMiner - associating enzyme EC numbers with Pfam domains

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

      gEMtools - GPU-accelerated 2D particle picking and 3D fitting for cryo-EM micrographs

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



      Selected Publications

      • Calculating and scoring high quality multiple flexible protein structure alignments. D.W. Ritchie (2016). Bioinformatics.
      • 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].
      • 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.
      • 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.
      • 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).
      • 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).
      • 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.
      • 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]
      • Protein Docking Using Spherical Polar Fourier Correlations, D.W. Ritchie, G.J.L. Kemp (2000) PROTEINS: Struct. Funct. Genet. 39, 178-194. [PDF]

      See All Publications, Presentations & Posters



      Habilitation Memoir (CNU Section 27 - Informatique)

      The "Habilitation" (HDR) is a French qualification giving the authority to supervise research students in association with a French university.

      • 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]
      • Inria news story about the HDR [link] (in French)


      Administrative Duties

      I am a member of the "bureau" of the Project Committee at Inria Nancy (which mainly concerns the evaluation of existing teams or proposals for new teams) and the LORIA's "Mention Informatique" Committee (which reviews requests to the Doctoral School).

      Previously I was a member of the "Comipers-Enseignants" (which reviews requests for sabbaticals and invited professors).



      Technology Transfer & Commercialisation

      I am one of the founders of Harmonic Pharma.

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



      Related Links

      • Université de Lorraine - Faculté des Sciences et Technologies
      • Informatics Masters - Université de Lorraine
      • 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
      • Campus France (international student portal)


      Publicity Material

      Video Presentation of KBDOCK - Knowledge-based Docking

      Capsid To The Rescue (in French)



      Inspirational Videos

      • Powering the Cell: Mitochondria by Harvard BioVisions and XVIVO
      • An Inconvenient Truth by Al Gore
      • Home - a film by Yann Arthus-Bertrand
      • Brian Cox on TED (on why funding research is a Good Thing)


      Living in France (for Foreigners)

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


      Outside of Work

      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

      Here are some pictures of some cool structures made by my brother:

      • Handspring Design

      I also like watching old Clint Eastwood westerns:

      • You Laughing At My Mule?


      Contact

      INRIA Nancy Grand Est
      615 Rue du Jardin Botanique
      54600 Villers-lès-Nancy, France
      Phone : +33 3 83 59 30 45
      E-mail: dave.ritchie AT inria.fr (please make your own AT sign)

      • Visitor Information


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