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  • The Inria's Research Teams produce an annual Activity Report presenting their activities and their results of the year. These reports include the team members, the scientific program, the software developed by the team and the new results of the year. The report also describes the grants, contracts and the activities of dissemination and teaching. Finally, the report gives the list of publications of the year.

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Major publications by the team in recent years
  • 1S. 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 ]
  • 2A. 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 ]
  • 3A. 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 ]
  • 4A. 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.
  • 5T. 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 ]
  • 6G. 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 ]
  • 7V. 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 ]
  • 8D. 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 ]
  • 9D. 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 ]
  • 10D. 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

Doctoral Dissertations and Habilitation Theses

Articles in International Peer-Reviewed Journals

  • 13S. Z. Alborzi, D. Ritchie, M.-D. Devignes.

    Computational Discovery of Direct Associations between GO terms and Protein Domains, in: BMC Bioinformatics, November 2018, vol. 19, no Suppl 14, 413 p. [ DOI : 10.1186/s12859-018-2380-2 ]
  • 14I. R. G. Caposi, D. R. Faria, K. M. Seiketa, F. Rodrigues, P. Bomfim-Mendonça, T. Becker, E. S. Kioshima, T. Svidzinski, B. Maigret.

    Repurposing Approach Identifies New Treatment Options for Invasive Fungal Disease, in: Bioorganic Chemistry, 2018. [ DOI : 10.1016/j.bioorg.2018.11.019 ]
  • 15S. Dey, D. Ritchie, E. D. Levy.

    PDB-wide identification of biological assemblies from conserved quaternary structure geometry, in: Nature Methods, 2018, vol. 15, pp. 67-72. [ DOI : 10.1038/nmeth.4510 ]
  • 16K. Ghania, B. Messabih, A. Chouarfia, B. Maigret.

    Flexible molecular docking: application of hybrid tabu-simplex optimisation, in: International journal of computational biology and drug design, 2018.
  • 17W. Inoubli, S. Aridhi, H. Mezni, M. Maddouri, E. Mephu Nguifo.

    An experimental survey on big data frameworks, in: Future Generation Computer Systems, September 2018, vol. 86, pp. 546 - 564. [ DOI : 10.1016/j.future.2018.04.032 ]
  • 18C. Krieger, S. Roselli, S. Kellner-Thielmann, G. Galati, B. Schneider, J. Grosjean, A. Olry, D. Ritchie, U. Matern, F. Bourgaud, A. Hehn.

    The CYP71AZ P450 Subfamily: A Driving Factor for the Diversification of Coumarin Biosynthesis in Apiaceous Plants, in: Frontiers in Plant Science, June 2018, vol. 9. [ DOI : 10.3389/fpls.2018.00820 ]
  • 19H. Mezni, S. Aridhi, A. Hadjali.

    The uncertain cloud: State of the art and research challenges, in: International Journal of Approximate Reasoning, December 2018, vol. 103, pp. 139 - 151. [ DOI : 10.1016/j.ijar.2018.09.009 ]

International Conferences with Proceedings

  • 20K. Dalleau, M. Couceiro, M. Smaïl-Tabbone.

    Unsupervised extremely randomized trees, in: PAKDD 2018 - The 22nd Pacific-Asia Conference on Knowledge Discovery and Data Mining, Melbourne, Australia, May 2018.
  • 21M.-D. Devignes, Y. Fransot, Y. Lepage, J. Lieber, E. Nauer, M. Smaïl-Tabbone.

    First steps toward finding relevant pathology-gene pairs using analogy, in: EvoCBR 2018 : Workshop on Evolutionary Computation and CBR at the International Conference on Case-Based Reasoning (ICCBR 2018), Stockholm, Sweden, July 2018.
  • 22W. Inoubli, S. Aridhi, H. Mezni, M. Maddouri, E. M. Nguifo.

    A Comparative Study on Streaming Frameworks for Big Data, in: VLDB 2018 - 44th International Conference on Very Large Data Bases : Workshop LADaS - Latin American Data Science, Rio de Janeiro, Brazil, August 2018, pp. 1-8.
  • 23G. Personeni, M.-D. Devignes, M. Smaïl-Tabbone, P. Jonveaux, C. Bonnet, A. Coulet.

    Cooperation of bio-ontologies for the classification of genetic intellectual disabilities : a diseasome approach, in: Proceedings of the 11th International Conference on Semantic Web Applications and Tools for Healthcare and Life Sciences (SWAT4HCLS 2018), Antwerp, Belgium, December 2018.
  • 24B. Sarker, D. W. Ritchie, S. Aridhi.

    Exploiting Complex Protein Domain Networks for Protein Function Annotation, in: Complex Networks 2018 - 7th International Conference on Complex Networks and Their Applications, Cambridge, United Kingdom, December 2018.

National Conferences with Proceedings

  • 25M. Zoghlami, S. Aridhi, M. Maddouri, E. M. Nguifo.

    ABClass : Une approche d'apprentissage multi-instances pour les séquences, in: RJCIA 2018 - 16èmes Rencontres des Jeunes Chercheurs en Intelligence Artificielle, Nancy, France, July 2018, pp. 1-9.

Scientific Books (or Scientific Book chapters)

  • 26M. Zoghlami, S. Aridhi, M. Maddouri, E. Mephu Nguifo.

    An Overview of in Silico Methods for the Prediction of Ionizing Radiation Resistance in Bacteria, in: Ionizing Radiation: Advances in Research and Applications, T. Reeve (editor), Physics Research and Technology Series, Nova science publishers, May 2018, pp. 241-256.

Other Publications

  • 27S. Z. Alborzi, S. Aridhi, D. Ritchie, M.-D. Devignes.

    PPI DomainMiner: predicting domain-domain interactions from protein-protein interactions using tripartite graph modeling and vector similarity, September 2018, ECCB 2018 - 17th European Conference on Computational Biology, Poster.
  • 28E. Bresso, C. Lacomblez, A. Pizard, P. Rossignol, F. Zannad, M. Smaïl-Tabbone, M.-D. Devignes.

    A data science approach for exploring differential expression profiles of genes in transcriptomic studies-Application to the understanding of ageing in obese and lean rats in the FIGHT-HF project, July 2018, JOBIM 2018 - Journées Ouvertes Biologie, Informatique et Mathématiques, Poster.
  • 29I. Chauvot de Beauchêne, S. J. De Vries.

    Reactive pipelines for integrated structural bioinformatics resources, October 2018, 3D-BioInfo: Launch Meeting for a proposed ELIXIR Community in Structural Bioinformatics, Poster.
  • 30D. Ritchie.

    Whole Number Recursion Formulae for High Order Clebsch-Gordan Coupling Coefficients, July 2018, working paper or preprint.
  • 31M. E. Ruiz­ Echartea, I. Chauvot de Beauchêne, D. Ritchie.

    EROS: A Protein Docking Algorithm Using a Quaternion Pi-Ball Representation for Exhaustive and Accelerated Exploration of 3D Rotational Space, November 2018, APIL 2018 - Journée d'automne de l'Ecole Doctorale IAEM-Lorraine, Poster.
  • 32B. Sarker, D. Ritchie, S. Aridhi.

    GrAPFI: Graph Based Inference for Automatic Protein Function Annotation, September 2018, ECCB 2018 - 17th European Conference on Computational Biology, Poster.
  • 33C. Singhal, Y. Ponty, I. Chauvot de Beauchêne.

    A hybrid combinatorial method for docking single stranded RNA on proteins at the thermodynamic equilibrium, April 2018, RECOMB 2018 - 22nd Annual International Conference on Research in Computational Molecular Biology, Poster.
References in notes
  • 34S. 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.
  • 35S. 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.
  • 36S. 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 ]
  • 37C. 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.
  • 38S. 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 ]
  • 39M. Baaden, S. R. Marrink.

    Coarse-grained modelling of protein-protein interactions, in: Current Opinion in Structural Biology, 2013, vol. 23, pp. 878–886.
  • 40A. Berchanski, M. Eisenstein.

    Construction of molecular assemblies via docking: modeling of tetramers with D2 symmetry, in: Proteins, 2003, vol. 53, pp. 817–829.
  • 41H. 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.
  • 42P. 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.
  • 43E. 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 ]
  • 44I. 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 ]
  • 45I. Chauvot de Beauchêne, 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.
  • 46C. 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 ]
  • 47P. 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.
  • 48K. 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.
  • 49S. 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 ]
  • 50M.-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.
  • 51W. 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/ ]
  • 52S. 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.
  • 53M. 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 ]
  • 54R. 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.
  • 55W. J. Frawley, G. Piatetsky-Shapiro, C. J. Matheus.

    Knowledge Discovery in Databases: An Overview, in: AI Magazine, 1992, vol. 13, pp. 57–70.
  • 56R. 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.
  • 57R. 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.
  • 58H. 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.
  • 59H. 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.
  • 60J. D. Jackson.

    Classical Electrodynamics, Wiley, New York, 1975.
  • 61P. J. Kundrotas, Z. W. Zhu, I. A. Vakser.

    GWIDD: Genome-wide protein docking database, in: Nucleic Acids Research, 2010, vol. 38, pp. D513–D517.
  • 62M. F. Lensink, S. J. Wodak.

    Docking and scoring protein interactions: CAPRI 2009, in: Proteins, 2010, vol. 78, pp. 3073–3084.
  • 63N. 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 ]
  • 64L. 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.
  • 65A. 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.
  • 66I. 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.
  • 67C. Morris.

    Towards a structural biology work bench, in: Acta Crystallographica, 2013, vol. PD69, pp. 681–682.
  • 68D. Mustard, D. Ritchie.

    Docking essential dynamics eigenstructures, in: Proteins: Structure, Function, and Genetics, 2005, vol. 60, pp. 269-274. [ DOI : 10.1002/prot.20569 ]
  • 69S. 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.
  • 70G. 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 ]
  • 71G. 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.
  • 72G. 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.
  • 73G. 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.
  • 74G. 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.
  • 75B. 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.
  • 76D. 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 ]
  • 77D. Ritchie, G. J. Kemp.

    Protein docking using spherical polar Fourier correlations, in: Proteins: Structure, Function, and Genetics, 2000, vol. 39, pp. 178-194.
  • 78D. 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 ]
  • 79D. 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 ]
  • 80A. 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.
  • 81S. 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 ]
  • 82M. E. Ruiz­ Echartea, I. Chauvot de Beauchêne, D. Ritchie.

    Accelerating Protein Docking Calculations using the ATTRACT Coarse­Grained Force Field and 3D Rotation Maps, May 2017, GGMM-2017, Poster.
  • 83M. G. Saunders, G. A. Voth.

    Coarse-graining of multiprotein assemblies, in: Current Opinion in Structural Biology, 2012, vol. 22, pp. 144–150.
  • 84D. 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.
  • 85M. L. Sierk, G. J. Kleywegt.

    Déjà vu all over again: Finding and analyzing protein structure similarities, in: Structure, 2004, vol. 12, pp. 2103–2011.
  • 86S. 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.
  • 87V. 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 ]
  • 88A. B. Ward, A. Sali, I. A. Wilson.

    Integrative Structural Biology, in: Biochemistry, 2013, vol. 6122, pp. 913–915.
  • 89S. Yang, P. E. Bourne.

    The Evolutionary History of Protein Domains Viewed by Species Phylogeny, in: PLoS One, 2009, vol. 4, e8378 p.
  • 90Q. 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.
  • 91H. 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 ]
  • 92A. 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.