Overall Objectives
Research Program
Application Domains
Highlights of the Year
New Software and Platforms
New Results
Partnerships and Cooperations
XML PDF e-pub
PDF e-Pub


Major publications by the team in recent years
A. W. Ghoorah, M.-D. Devignes, M. Smaïl-Tabbone, D. Ritchie.
Spatial clustering of protein binding sites for template based protein docking, in: Bioinformatics, August 2011, vol. 27, no 20, pp. 2820-2827. [ DOI : 10.1093/bioinformatics/btr493 ]
A. W. Ghoorah, M.-D. Devignes, M. Smaïl-Tabbone, D. Ritchie.
Protein Docking Using Case-Based Reasoning, in: Proteins, October 2013, vol. 81, no 12, pp. 2150-2158. [ DOI : 10.1002/prot.24433 ]
A. W. Ghoorah, M.-D. Devignes, M. Smaïl-Tabbone, D. Ritchie.
KBDOCK 2013: A spatial classification of 3D protein domain family interactions, in: Nucleic Acids Research, January 2014, vol. 42, no D1, pp. 389-395.
T. V. Hoang, X. Cavin, D. Ritchie.
gEMfitter: A highly parallel FFT-based 3D density fitting tool with GPU texture memory acceleration, in: Journal of Structural Biology, September 2013. [ DOI : 10.1016/j.jsb.2013.09.010 ]
T. Hoang, X. Cavin, P. Schultz, D. Ritchie.
gEMpicker: a highly parallel GPU-accelerated particle picking tool for cryo-electron microscopy, in: BMC Structural Biology, 2013, vol. 13, no 1, 25 p. [ DOI : 10.1186/1472-6807-13-25 ]
G. Macindoe, L. Mavridis, V. Venkatraman, M.-D. Devignes, D. Ritchie.
HexServer: an FFT-based protein docking server powered by graphics processors, in: Nucleic Acids Research, May 2010, vol. 38, pp. W445-W449. [ DOI : 10.1093/nar/gkq311 ]
V. Pérez-Nueno, A. S. Karaboga, M. Souchet, D. Ritchie.
GESSE: Predicting Drug Side Effects from Drug–Target Relationships, in: Journal of Chemical Information and Modeling, August 2015, vol. 55, no 9, pp. 1804-1823. [ DOI : 10.1021/acs.jcim.5b00120 ]
D. W. Ritchie, S. Grudinin.
Spherical polar Fourier assembly of protein complexes with arbitrary point group symmetry, in: Journal of Applied Crystallography, February 2016, vol. 49, no 1, pp. 158-167. [ DOI : 10.1107/S1600576715022931 ]
D. Ritchie.
Calculating and scoring high quality multiple flexible protein structure alignments, in: Bioinformatics, May 2016, vol. 32, no 17, pp. 2650-2658. [ DOI : 10.1093/bioinformatics/btw300 ]
D. W. Ritchie, V. Venkatraman.
Ultra-fast FFT protein docking on graphics processors, in: Bioinformatics, August 2010, vol. 26, no 19, pp. 2398-2405. [ DOI : 10.1093/bioinformatics/btq444 ]
Publications of the year

Articles in International Peer-Reviewed Journals

S. Z. Alborzi, M.-D. Devignes, D. W. Ritchie.
ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains, in: BMC Bioinformatics, December 2017, vol. 18, no 1, 107 p. [ DOI : 10.1186/s12859-017-1519-x ]
S. Aridhi, A. Montresor, Y. Velegrakis.
BLADYG: A Graph Processing Framework for Large Dynamic Graphs, in: Big Data Research, 2017, [ DOI : 10.1016/j.bdr.2017.05.003 ]
C. Chamard-Jovenin, C. Thiebaut, A. Chesnel, E. Bresso, C. Morel, M. Smaïl-Tabbone, M.-D. Devignes, T. Boukhobza, H. Dumond.
Low-dose alkylphenol exposure promotes mammary epithelium alterations and transgenerational developmental defects, but does not enhance tumorigenic behaviour of breast cancer cells, in: Frontiers in Endocrinology, October 2017, vol. 8, 272 p. [ DOI : 10.3389/fendo.2017.00272 ]
C. Coluzzi, G. Guédon, M.-D. Devignes, C. Ambroset, V. Loux, S. Payot, N. N. Leblond-Bourget, T. Lacroix.
A Glimpse into the World of Integrative and Mobilizable Elements in Streptococci Reveals an Unexpected Diversity and Novel Families of Mobilization Proteins, in: Frontiers in Microbiology, March 2017, vol. 8, 16 p. [ DOI : 10.3389/fmicb.2017.00443 ]
P. Couvineau, H. de Almeida, B. Maigret, C. Llorens-Cortes, X. Iturrioz.
Involvement of arginine 878 together with Ca2+ in aminopeptidase A substrate specificity for N-terminal acidic amino-acid residues, in: PLoS ONE, September 2017.
S. Dey, D. Ritchie, E. D. Levy.
PDB-wide identification of biological assemblies from conserved quaternary structure geometry, in: Nature Methods, November 2017, pp. 1-20. [ DOI : 10.1038/nmeth.4510 ]
W. Dhifli, S. Aridhi, E. Mephu Nguifo.
MR-SimLab: Scalable subgraph selection with label similarity for big data, in: Information Systems, 2017, vol. 69, pp. 155 - 163. [ DOI : 10.1016/ ]
M. El Houasli, B. Maigret, M.-D. Devignes, A. W. Ghoorah, S. Grudinin, D. Ritchie.
Modeling and minimizing CAPRI round 30 symmetrical protein complexes from CASP-11 structural models, in: Proteins: Structure, Function, and Genetics, March 2017, vol. 85, no 3, pp. 463–469. [ DOI : 10.1002/prot.25182 ]
N. E. I. Karabadji, H. Seridi, F. Bousetouane, W. Dhifli, S. Aridhi.
An evolutionary scheme for decision tree construction, in: Knowledge-Based Systems, March 2017, vol. 119, pp. 166 - 177. [ DOI : 10.1016/j.knosys.2016.12.011 ]
G. Personeni, E. Bresso, M.-D. Devignes, M. Dumontier, M. Smaïl-Tabbone, A. Coulet.
Discovering associations between adverse drug events using pattern structures and ontologies, in: Journal of Biomedical Semantics, 2017, vol. 93, pp. 539 - 546. [ DOI : 10.1038/clpt.2013.24 ]
S. Roselli, A. Olry, S. Vautrin, O. O. Coriton, D. Ritchie, G. Galati, N. Navrot, C. Krieger, G. Vialart, H. H. Berges, F. Bourgaud, A. Hein.
A bacterial artificial chromosome (BAC) genomic approach reveals partial clustering of the furanocoumarin pathway genes in parsnip, in: Plant Journal, February 2017, vol. 89, no 6, pp. 1119-1132. [ DOI : 10.1111/tpj.13450 ]

International Conferences with Proceedings

S. Z. Alborzi, S. Aridhi, M.-D. Devignes, R. Saidi, A. Renaux, M. J. Martin, D. W. Ritchie.
Automatic Generation of Functional Annotation Rules Using Inferred GO-Domain Associations, in: Function-SIG ISMB/ECCB 2017, Prague, Czech Republic,, July 2017.
S. Z. Alborzi, M.-D. Devignes, D. Ritchie.
Associating Gene Ontology Terms with Pfam Protein Domains, in: 5th International Work-Conference on Bioinformatics and Biomedical Engineering - IWBBIO 2017, Granada, Spain, I. Rojas, F. Ortuño (editors), Bioinformatics and Biomedical Engineering, Springer, April 2017, vol. 10209, pp. 127-138. [ DOI : 10.1007/978-3-319-56154-7_13 ]

Other Publications

S. Z. Alborzi, M.-D. Devignes, S. Aridhi, R. Saidi, A. Renaux, M. J. Martin, D. W. Ritchie.
Automatic Generation of Functional Annotation Rules Using Inferred GO-Domain Associations, July 2017, Function-SIG ISMB/ECCB 2017, Poster.
S. Aridhi, S. Z. Alborzi, M. Smaïl-Tabbone, M.-D. Devignes, D. Ritchie.
Neighborhood-Based Label Propagation in Large Protein Graphs, July 2017, 2 p, Function SIG @ ISMB/ECCB 2017, Poster.
References in notes
C. E. Alvarez-Martinez, P. J. Christie.
Biological diversity of prokaryotic type IV secretion systems, in: Microbiology and Molecular Biology Reviews, 2011, vol. 73, pp. 775–808.
M. Baaden, S. R. Marrink.
Coarse-grained modelling of protein-protein interactions, in: Current Opinion in Structural Biology, 2013, vol. 23, pp. 878–886.
A. Berchanski, M. Eisenstein.
Construction of molecular assemblies via docking: modeling of tetramers with D2 symmetry, in: Proteins, 2003, vol. 53, pp. 817–829.
H. M. Berman, T. Battistuz, T. N. Bhat, W. F. Bluhm, P. E. Bourne, K. Burkhardt, Z. Feng, G. L. Gilliland, L. Iype, S. Jain, P. Fagan, J. Marvin, D. Padilla, V. Ravichandran, B. Schneider, N. Thanki, H. Weissig, J. D. Westbrook, C. Zardecki.
The Protein Data Bank, in: Acta. Cryst., 2002, vol. D58, pp. 899–907.
P. Bork, L. J. Jensen, C. von Mering, A. K. Ramani, I. Lee, E. M. Marcotte.
Protein interaction networks from yeast to human, in: Current Opinion in Structural Biology, 2004, vol. 14, pp. 292–299.
E. Bresso, V. Leroux, M. Urban, K. Hammond-Kosack, B. Maigret, N. F. Martins.
Structure-based virtual screening of hypothetical inhibitors of the enzyme longiborneol synthase-a potential target to reduce Fusarium head blight disease, in: Journal of Molecular Modeling, July 2016, vol. 22, no 7. [ DOI : 10.1007/s00894-016-3021-1 ]
I. J. Chauvot De Beauchene, S. J. De Vries, M. J. Zacharias.
Fragment-based modeling of protein-bound ssRNA, September 2016, ECCB 2016: The 15th European Conference on Computational Biology, Poster.
I. Chauvot de Beauchêne, S. J. De Vries, M. Zacharias.
Fragment-based modelling of single stranded RNA bound to RNA recognition motif containing proteins, in: Nucleic Acids Research, June 2016. [ DOI : 10.1093/nar/gkw328 ]
K. Dalleau, M. Couceiro, M.-D. Devignes, C. Raïssi, M. Smaïl-Tabbone.
Using aggregation functions on structured data: a use case in the FIGHT-HF project, in: International Symposium on Aggregation and Structures (ISAS 2016) , Luxembourg, Luxembourg, G. Kiss, J.-L. Marichal, B. Teheux (editors), International Symposium on Aggregation and Structures (ISAS 2016) - Book of abstracts, July 2016.
S. J. De Vries, I. Chauvot de Beauchêne, c. E. M. Schindler, M. Zacharias.
Cryo-EM Data Are Superior to Contact and Interface Information in Integrative Modeling, in: Biophysical Journal, February 2016. [ DOI : 10.1016/j.bpj.2015.12.038 ]
M.-D. Devignes, B. Sidahmed, M. Smaïl-Tabbone, N. Amedeo, P. Olivier.
Functional classification of genes using semantic distance and fuzzy clustering approach: Evaluation with reference sets and overlap analysis, in: international Journal of Computational Biology and Drug Design. Special Issue on: ”Systems Biology Approaches in Biological and Biomedical Research”, 2012, vol. 5, no 3/4, pp. 245-260.
S. E. Dobbins, V. I. Lesk, M. J. E. Sternberg.
Insights into protein flexibility: The relationship between normal modes and conformational change upon protein–protein docking, in: Proceedings of National Academiy of Sciences, 2008, vol. 105, no 30, pp. 10390–10395.
R. D. Finn, J. Mistry, J. Tate, P. Coggill, A. Heger, J. E. Pollington, O. L. Gavin, P. Gunasekaran, G. Ceric, K. Forslund, L. Holm, E. L. L. Sonnhammer, S. R. Eddy, A. Bateman.
The Pfam protein families database, in: Nucleic Acids Research, 2010, vol. 38, pp. D211–D222.
W. J. Frawley, G. Piatetsky-Shapiro, C. J. Matheus.
Knowledge Discovery in Databases: An Overview, in: AI Magazine, 1992, vol. 13, pp. 57–70.
R. Fronzes, E. Schäfer, L. Wang, H. R. Saibil, E. V. Orlova, G. Waksman.
Structure of a type IV secretion system core complex, in: Science, 2011, vol. 323, pp. 266–268.
R. A. Goldstein.
The structure of protein evolution and the evolution of proteins structure, in: Current Opinion in Structural Biology, 2008, vol. 18, pp. 170–177.
H. Hermjakob, L. Montecchi-Palazzi, G. Bader, J. Wojcik, L. Salwinski, A. Ceol, S. Moore, S. Orchard, U. Sarkans, C. von Mering, B. Roechert, S. Poux, E. Jung, H. Mersch, P. Kersey, M. Lappe, Y. Li, R. Zeng, D. Rana, M. Nikolski, H. Husi, C. Brun, K. Shanker, S. G. N. Grant, C. Sander, P. Bork, W. Zhu, A. Pandey, A. Brazma, B. Jacq, M. Vidal, D. Sherman, P. Legrain, G. Cesareni, I. Xenarios, D. Eisenberg, B. Steipe, C. Hogue, R. Apweiler.
The HUPO PSI's Molecular Interaction format – a community standard for the representation of protein interaction data, in: Nature Biotechnology, 2004, vol. 22, no 2, pp. 177-183.
H. I. Ingólfsson, C. A. Lopez, J. J. Uusitalo, D. H. de jong, S. M. Gopal, X. Periole, S. R. Marrink.
The power of coarse graining in biomolecular simulations, in: WIRES Comput. Mol. Sci., 2013, vol. 4, pp. 225–248.
J. D. Jackson.
Classical Electrodynamics, Wiley, New York, 1975.
P. J. Kundrotas, Z. W. Zhu, I. A. Vakser.
GWIDD: Genome-wide protein docking database, in: Nucleic Acids Research, 2010, vol. 38, pp. D513–D517.
M. F. Lensink, S. J. Wodak.
Docking and scoring protein interactions: CAPRI 2009, in: Proteins, 2010, vol. 78, pp. 3073–3084.
N. F. Martins, E. Bresso, R. C. Togawa, M. Urban, J. Antoniw, B. Maigret, K. Hammond-Kosack.
Searching for Novel Targets to Control Wheat Head Blight Disease-I-Protein Identification, 3D Modeling and Virtual Screening, in: Advances in Microbiology, September 2016, vol. 06, no 11, pp. 811 - 830. [ DOI : 10.4236/aim.2016.611079 ]
L. Mavridis, V. Venkatraman, D. W. Ritchie.
A Comprehensive Comparison of Protein Structural Alignment Algorithms, in: 3DSIG – 8th Structural Bioinformatics and Computational Biophysics Meeting, Long Beach, California, ISMB, 2012, vol. 8, 89 p.
A. May, M. Zacharias.
Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking, in: Proteins, 2008, vol. 70, pp. 794–809.
I. H. Moal, P. A. Bates.
SwarmDock and the Use of Normal Modes in Protein-Protein Docking, in: International Journal of Molecular Sciences, 2010, vol. 11, no 10, pp. 3623–3648.
C. Morris.
Towards a structural biology work bench, in: Acta Crystallographica, 2013, vol. PD69, pp. 681–682.
D. Mustard, D. Ritchie.
Docking essential dynamics eigenstructures, in: Proteins: Structure, Function, and Genetics, 2005, vol. 60, pp. 269-274. [ DOI : 10.1002/prot.20569 ]
S. Orchard, S. Kerrien, S. Abbani, B. Aranda, J. Bhate, S. Bidwell, A. Bridge, L. Briganti, F. S. L. Brinkman, G. Cesareni, A. Chatraryamontri, E. Chautard, C. Chen, M. Dumousseau, J. Goll, R. E. W. Hancock, L. I. Hannick, I. Jurisica, J. Khadake, D. J. Lynn, U. Mahadevan, L. Perfetto, A. Raghunath, S. Ricard-Blum, B. Roechert, L. Salwinski, V. Stümpflen, M. Tyers, P. Uetz, I. Xenarios, H. Hermjakob.
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium, in: Nature Methods, 2012, vol. 9, no 4, pp. 345-350.
G. Personeni, S. Daget, C. Bonnet, P. Jonveaux, M.-D. Devignes, M. Smaïl-Tabbone, A. Coulet.
ILP for Mining Linked Open Data: a biomedical Case Study, in: The 24th International Conference on Inductive Logic Programming (ILP 2014), Nancy, France, September 2014.
G. Personeni, S. Daget, C. Bonnet, P. Jonveaux, M.-D. Devignes, M. Smaïl-Tabbone, A. Coulet.
Mining Linked Open Data: A Case Study with Genes Responsible for Intellectual Disability, in: Data Integration in the Life Sciences - 10th International Conference, DILS 2014, Lisbon, Portugal, H. Galhardas, E. Rahm (editors), Lecture Notes in Computer Science, Springer, 2014, vol. 8574, pp. 16 - 31.
G. Personeni, M.-D. Devignes, M. Dumontier, M. Smaïl-Tabbone, A. Coulet.
Discovering ADE associations from EHRs using pattern structures and ontologies, in: Phenotype Day, Bio-Ontologies SIG, ISMB, Orlando, United States, July 2016.
G. Personeni, M.-D. Devignes, M. Dumontier, M. Smaïl-Tabbone, A. Coulet.
Extraction d'association d'EIM à partir de dossiers patients : expérimentation avec les structures de patrons et les ontologies, in: Deuxième Atelier sur l'Intelligence Artificielle et la Santé, Montpellier, France, Atelier IA & Santé, June 2016.
B. Pierce, W. Tong, Z. Weng.
M-ZDOCK: A Grid-Based Approach for Cn Symmetric Multimer Docking, in: Bioinformatics, 2005, vol. 21, no 8, pp. 1472–1478.
D. Ritchie, A. Ghoorah, L. Mavridis, V. Venkatraman.
Fast Protein Structure Alignment using Gaussian Overlap Scoring of Backbone Peptide Fragment Similarity, in: Bioinformatics, October 2012, vol. 28, no 24, pp. 3274-3281. [ DOI : 10.1093/bioinformatics/bts618 ]
D. Ritchie, G. J. Kemp.
Protein docking using spherical polar Fourier correlations, in: Proteins: Structure, Function, and Genetics, 2000, vol. 39, pp. 178-194.
D. Ritchie, D. Kozakov, S. Vajda.
Accelerating and focusing protein–protein docking correlations using multi-dimensional rotational FFT generating functions, in: Bioinformatics, June 2008, vol. 24, no 17, pp. 1865-1873. [ DOI : 10.1093/bioinformatics/btn334 ]
D. Ritchie.
Recent Progress and Future Directions in Protein-Protein Docking, in: Current Protein and Peptide Science, February 2008, vol. 9, no 1, pp. 1-15. [ DOI : 10.2174/138920308783565741 ]
A. Rivera-Calzada, R. Fronzes, C. G. Savva, V. Chandran, P. W. Lian, T. Laeremans, E. Pardon, J. Steyaert, H. Remaut, G. Waksman, E. V. Orlova.
Structure of a bacterial type IV secretion core complex at subnanometre resolution, in: EMBO Journal, 2013, vol. 32, pp. 1195–1204.
M. G. Saunders, G. A. Voth.
Coarse-grainiing of multiprotein assemblies, in: Current Opinion in Structural Biology, 2012, vol. 22, pp. 144–150.
D. Schneidman-Duhovny, Y. Inbar, R. Nussinov, H. J. Wolfson.
Geometry-based flexible and symmetric protein docking, in: Proteins, 2005, vol. 60, no 2, pp. 224–231.
M. L. Sierk, G. J. Kleywegt.
Déjà vu all over again: Finding and analyzing protein structure similarities, in: Structure, 2004, vol. 12, pp. 2103–2011.
S. Velankar, J. M. Dana, J. Jacobsen, G. van Ginkel, P. J. Gane, J. Luo, T. J. Oldfield, C. O'Donovan, M.-J. Martin, G. J. Kleywegt.
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource, in: Nucleic Acids Research, 2012, vol. 41, pp. D483–D489.
V. Venkatraman, D. Ritchie.
Flexible protein docking refinement using pose-dependent normal mode analysis, in: Proteins, June 2012, vol. 80, no 9, pp. 2262-2274. [ DOI : 10.1002/prot.24115 ]
A. B. Ward, A. Sali, I. A. Wilson.
Integrative Structural Biology, in: Biochemistry, 2013, vol. 6122, pp. 913–915.
S. Yand, P. E. Bourne.
The Evolutionary History of Protein Domains Viewed by Species Phylogeny, in: PLoS One, 2009, vol. 4, e8378.
Q. C. Zhang, D. Petrey, L. Deng, L. Qiang, Y. Shi, C. A. Thu, B. Bisikirska, C. Lefebvre, D. Accili, T. Hunter, T. Maniatis, A. Califano, B. Honig.
Structure-based prediction of protein-protein interactions on a genome-wide scale, in: Nature, 2012, vol. 490, pp. 556–560.
H. de Almeida, V. Leroux, F. N. Motta, P. Grellier, B. Maigret, J. M. Santana, I. M. D. Bastos.
Identification of novel Trypanosoma cruzi prolyl oligopeptidase inhibitors by structure-based virtual screening, in: Journal of Computer-Aided Molecular Design, October 2016. [ DOI : 10.1007/s10822-016-9985-1 ]
A. Özgur, Z. Xiang, D. R. Radev, Y. He.
Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology, in: Journal of Biomedical Semantics, 2011, vol. 2 (Suppl 2), S8 p.