Dave Ritchie

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 Pictures

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.

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 - new! - for protein complexes with arbitrary point group symmetry

Kpax - protein structure alignment - version 5 now available! - for pair-wise and multiple alignments with or without flexibility

ECDomainMiner - new! - 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

• 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

• 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)

I am a member of the "bureau" of the Project Committee at Inria Nancy 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).

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

• 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)

• 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)

• 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, 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?

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