Computational Algorithms for Protein Structures and Interactions
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
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
Probability Theory Applied to Evolutionary Biology - Benoit Henry
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.
This year, we are proposing two PhD thesis projects (deadline 30/03/2017):
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
for protein complexes with arbitrary point group symmetry
- Clebsch-Gordan coefficient calculator- new!
- protein structure alignment - version 5 now available!
- for pair-wise and multiple alignments with or without flexibility
- new! - protein sequence to EC number annotation by graph label propagation
- associating enzyme EC numbers with Pfam domains
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 "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
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)