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 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

• 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 (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).

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