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Bibliography

Major publications by the team in recent years
  • 1A. 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 ]

    https://hal.inria.fr/inria-00617921
  • 2A. 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 ]

    https://hal.inria.fr/hal-00880341
  • 3A. 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.

    https://hal.inria.fr/hal-00920612
  • 4T. 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 ]

    https://hal.inria.fr/hal-00866871
  • 5T. 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 ]

    https://hal.inria.fr/hal-00955580
  • 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 ]

    https://hal.inria.fr/inria-00522712
  • 7D. 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 ]

    https://hal.inria.fr/hal-00756813
  • 8D. 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 ]

    https://hal.inria.fr/inria-00537988
  • 9V. 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 ]

    https://hal.inria.fr/hal-00756809
  • 10V. Venkatraman, D. W. Ritchie.

    Predicting Multi-component Protein Assemblies Using an Ant Colony Approach, in: International Journal of Swarm Intelligence Research, September 2012, vol. 3, pp. 19-31. [ DOI : 10.4018/jsir.2012070102 ]

    https://hal.inria.fr/hal-00756807
Publications of the year

Articles in International Peer-Reviewed Journals

  • 11C. Ambroset, C. Coluzzi, G. Guédon, M.-D. Devignes, V. Loux, T. Lacroix, S. Payot, N. Leblond-Bourget.

    New Insights into the Classification and Integration Specificity of Streptococcus Integrative Conjugative Elements through Extensive Genome Exploration, in: Frontiers in microbiology, January 2016, vol. 6, 1483 p. [ DOI : 10.3389/fmicb.2015.01483 ]

    https://hal.archives-ouvertes.fr/hal-01262284
  • 12T. Bourquard, F. Landomiel, E. Reiter, P. Crépieux, D. W. Ritchie, J. Azé, A. Poupon.

    Unraveling the molecular architecture of a G protein-coupled receptor/β-arrestin/Erk module complex, in: Scientific Reports, June 2015, 5:10760 p. [ DOI : 10.1038/srep10760 ]

    http://hal-lirmm.ccsd.cnrs.fr/lirmm-01162594
  • 13R. Gerbier, V. Leroux, P. Couvineau, R. Alvear-Perez, B. Maigret, C. Llorens-Cortes, X. Iturrioz.

    New structural insights into the apelin receptor: identification of key residues for apelin binding, in: FASEB Journal, January 2015, vol. 29, no 1, pp. 314-322. [ DOI : 10.1096/fj.14-256339 ]

    https://hal.inria.fr/hal-01251633
  • 14A. Ghoorah, M.-D. Devignes, S. Z. Alborzi, M. Smaïl-Tabbone, D. Ritchie.

    A Structure-Based Classification and Analysis of Protein Domain Family Binding Sites and Their Interactions, in: Biology, April 2015, vol. 4, no 2, pp. 327-343. [ DOI : 10.3390/biology4020327 ]

    https://hal.inria.fr/hal-01216748
  • 15V. 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 ]

    https://hal.inria.fr/hal-01216493
  • 16D. 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. [ DOI : 10.1107/S1600576715022931 ]

    https://hal.inria.fr/hal-01261402
  • 17A. K. Rodrigues Adabio, E. S. Kioshima, V. Leroux, N. F. Martins, B. Maigret, M. S. soares Felipe.

    Identification of New Antifungal Compounds Targeting Thioredoxin Reductase of Paracoccidioides Genus, in: PloS One, November 2015, vol. 10, no 11, e0142926. [ DOI : 10.1371/journal.pone.0142926 ]

    https://hal.inria.fr/hal-01251619

Articles in Non Peer-Reviewed Journals

  • 18M.-D. Devignes, M. Smaïl-Tabbone, D. Ritchie.

    Kbdock - Searching and organising the structural space of protein-protein interactions, in: ERCIM News, January 2016, no 104, pp. 24-25.

    https://hal.inria.fr/hal-01258117

International Conferences with Proceedings

  • 19S. Z. Alborzi, M.-D. Devignes, D. Ritchie.

    EC-PSI: Associating Enzyme Commission Numbers with Pfam Domains, in: JOBIM 2015, Clermont-Ferrand, France, July 2015. [ DOI : 10.1101/022343 ]

    https://hal.inria.fr/hal-01216743
References in notes
  • 20C. 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.
  • 21M. Baaden, S. R. Marrink.

    Coarse-grained modelling of protein-protein interactions, in: Current Opinion in Structural Biology, 2013, vol. 23, pp. 878–886.
  • 22A. Berchanski, M. Eisenstein.

    Construction of molecular assemblies via docking: modeling of tetramers with D2 symmetry, in: Proteins, 2003, vol. 53, pp. 817–829.
  • 23H. 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.
  • 24P. 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.
  • 25M.-D. Devignes, B. Sidahmed, M. Smail-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.

    https://hal.inria.fr/hal-00734329
  • 26S. 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.
  • 27D. Filmore.

    It's a GPCR world, in: Modern Drug Discovery, 2004, vol. 7, pp. 24–28.
  • 28R. 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.
  • 29W. J. Frawley, G. Piatetsky-Shapiro, C. J. Matheus.

    Knowledge Discovery in Databases: An Overview, in: AI Magazine, 1992, vol. 13, pp. 57–70.
  • 30R. 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.
  • 31A. G. Gilman.

    G proteins: transducers of receptor-generated signaling, in: Annual Review of Biochemistry, 1987, vol. 56, pp. 615–649.
  • 32R. 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.
  • 33H. 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.
  • 34H. 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.

    http://dx.doi.org/10.1002/wcms.1169
  • 35J. D. Jackson.

    Classical Electrodynamics, Wiley, New York, 1975.
  • 36J. Janin, K. Henrick, J. Moult, L. Ten Eyck, M. J. E. Sternberg, S. Vajda, I. Vakser, S. J. Wodak.

    CAPRI: A critical assessment of PRedicted Interactions, in: Proteins, 2003, vol. 52, pp. 2–9.
  • 37P. J. Kundrotas, Z. W. Zhu, I. A. Vakser.

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

    Docking and scoring protein interactions: CAPRI 2009, in: Proteins, 2010, vol. 78, pp. 3073–3084.
  • 39L. 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.
  • 40A. 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.
  • 41I. Moal, P. 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.
  • 42C. Morris.

    Towards a structural biology work bench, in: Acta Crystallographica, 2013, vol. PD69, pp. 681–682.
  • 43D. Mustard, D. Ritchie.

    Docking essential dynamics eigenstructures, in: Proteins: Structure, Function, and Genetics, 2005, vol. 60, pp. 269-274. [ DOI : 10.1002/prot.20569 ]

    https://hal.inria.fr/inria-00434271
  • 44S. 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.
  • 45G. 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.

    https://hal.inria.fr/hal-01095597
  • 46G. 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, E. R. Helena Galhardas (editor), Lecture Notes in Computer Science, Springer, 2014, vol. 8574, pp. 16 - 31.

    https://hal.inria.fr/hal-01095591
  • 47B. 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.
  • 48D. Ritchie, G. J. Kemp.

    Protein docking using spherical polar Fourier correlations, in: Proteins: Structure, Function, and Genetics, 2000, vol. 39, pp. 178-194.

    https://hal.inria.fr/inria-00434273
  • 49D. 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 ]

    https://hal.inria.fr/inria-00434264
  • 50D. 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 ]

    https://hal.inria.fr/inria-00434268
  • 51A. 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.
  • 52M. G. Saunders, G. A. Voth.

    Coarse-grainiing of multiprotein assemblies, in: Current Opinion in Structural Biology, 2012, vol. 22, pp. 144–150.
  • 53D. 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.
  • 54M. L. Sierk, G. J. Kleywegt.

    Déjà vu all over again: Finding and analyzing protein structure similarities, in: Structure, 2004, vol. 12, pp. 2103–2011.
  • 55M. Smaïl-Tabbone.

    Contribution to knowledge extraction from biological data, Université de Lorraine, November 2014, Habilitation à diriger des recherches.

    https://hal.inria.fr/tel-01093943
  • 56S. 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.
  • 57A. B. Ward, A. Sali, I. A. Wilson.

    Integrative Structural Biology, in: Biochemistry, 2013, vol. 6122, pp. 913–915.
  • 58S. Yand, P. E. Bourne.

    The Evolutionary History of Protein Domains Viewed by Species Phylogeny, in: PLoS One, 2009, vol. 4, e8378.
  • 59Q. 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.
  • 60A. 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.


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