High Performance Algorithms for Structural Systems Biology
I am responsible for the Capsid research team at the
Inria Nancy research centre in Nancy, France.
The team is common ("Equipe Projet Commun") to the CNRS, Inria, and the University of Lorraine.
People and Projects
Modeling Evolutionary Relationships Between Three Dimensional Protein Structures - Benoit Henry -
(with Nicolas Champagnat)
Former Students and Postdocs
I do not currently have funded vacancies, but please see below.
Each year, INRIA funds a number of doctoral thesis and postdoc projects.
These are awarded on a competitive basis.
PhD positions and
In a similar manner, the IAEM doctoral school
funds some doctoral theses in informatics.
Each year, INRIA supports a good number of internships (normally at masters-level)
in collaboration with foreign universities.
These opportunities are posted in the partner institutes in December. Please see:
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)
- run Hex on our GPU-powered server
- symmetry assembler program - new!
- for protein complexes with arbitrary point group symmetry
- protein structure alignment - version 4.0.0 now available!
- for pair-wise and multiple alignments with or without flexibility
KBDOCK Knowledge-Based Docking
- database of 3D protein interactions and binding sites
- 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).
Spherical Polar Fourier Assembly of Protein Complexes with Arbitrary Point Group Symmetry.
D.W. Ritchie and S. Grudinin (2016).
Journal of Applied Crystallography,
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.
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,
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
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
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
Protein Docking Using Spherical Polar Fourier Correlations,
D.W. Ritchie, G.J.L. Kemp (2000)
PROTEINS: Struct. Funct. Genet.
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
English: High Performance Algorithms for Molecular Shape Recognition
Collected papers 1999-2010
Inria news story about the HDR
[link] (in French)
I am a member of the
(which reviews requests for sabbaticals and invited professors).
Technology Transfer & Commercialisation
I am one of the founders of
My molecular shape-matching program "ParaFit" is marketed by
Living in France (for Foreigners)
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
mainly in the
Now, I very much like
Here are some pictures of some cool structures made by my brother:
I also like watching old Clint Eastwood westerns:
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)