Bibliography

Major publications by the team in recent years

• 1A. 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, n^o 20, pp. 2820-2827. [ DOI : 10.1093/bioinformatics/btr493 ]
  
  https://hal.inria.fr/inria-00617921
• 2A. W. Ghoorah, M.-D. Devignes, M. Smaïl-Tabbone, D. Ritchie.
  
  Protein Docking Using Case-Based Reasoning, in: Proteins, October 2013, vol. 81, n^o 12, pp. 2150-2158. [ DOI : 10.1002/prot.24433 ]
  
  https://hal.inria.fr/hal-00880341
• 3A. 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, n^o 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, n^o 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
• 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, n^o 9, pp. 1804-1823. [ DOI : 10.1021/acs.jcim.5b00120 ]
  
  https://hal.inria.fr/hal-01216493
• 8D. Ritchie.
  
  Calculating and scoring high quality multiple flexible protein structure alignments, in: Bioinformatics, May 2016, vol. 32, n^o 17, pp. 2650-2658. [ DOI : 10.1093/bioinformatics/btw300 ]
  
  https://hal.inria.fr/hal-01371083
• 9D. W. Ritchie, V. Venkatraman.
  
  Ultra-fast FFT protein docking on graphics processors, in: Bioinformatics, August 2010, vol. 26, n^o 19, pp. 2398-2405. [ DOI : 10.1093/bioinformatics/btq444 ]
  
  https://hal.inria.fr/inria-00537988
• 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
• 12E. Bresso, V. Leroux, M. Urban, K. E. 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, n^o 7. [ DOI : 10.1007/s00894-016-3021-1 ]
  
  https://hal.inria.fr/hal-01392851
• 13M. 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, October 2016. [ DOI : 10.1002/prot.25182 ]
  
  https://hal.inria.fr/hal-01388654
• 14M. F. Lensink, S. Velankar, A. Kryshtafovych, S.-Y. Huang, D. Schneidman-Duhovy, A. Sali, J. Segura, N. Fernandez-Fuentes, S. Viswanath, R. Elber, S. Grudinin, P. Popov, E. Neveu, H. Lee, M. Baek, S. Park, L. Heo, G. R. Lee, C. Seok, S. Qin, H.-X. Zhou, D. W. Ritchie, B. Maigret, M.-D. Devignes, A. Ghoorah, M. Torchala, R. A.G. Chaleil, P. A. Bates, E. Ben-Zeev, M. Eisenstein, S. Negi S., T. Vreven, B. G. Pierce, T. M. Borrman, J. Yu, F. Ochsenbein, Z. Weng, R. Guerois, A. Vangone, J. P. Rodrigues, G. van Zundert, M. Nellen, L. Xue, E. Karaca, A. S. J. Melquiond, K. Visscher, P. L. Kastritis, A. M. J. J. Bonvin, X. Xu, L. Qiu, C. Yan, J. Li, Z. Ma, J. Cheng, X. Zou, Y. Sheng, L. X. Peterson, H.-R. Kim, A. Roy, X. Han, J. Esquivel-Rodríguez, D. Kihara, X. Yu, N. J. Bruce, J. C. Fuller, R. C. Wade, I. Anishchenko, P. J. Kundrotas, I. A. Vakser, K. Imai, K. Yamada, T. Oda, T. Nakamura, K. Tomii, C. Pallara, M. Romero-Durana, B. Jiménez-García, I. H. Moal, J. Fernández-Recio, J. Y. Joung, J. Y. Kim, K. Joo, J. Lee, D. Kozakov, S. Vajda, S. Mottarella, D. R. Hall, D. Beglov, A. Mamonov, B. Xia, T. Bohnuud, C. A. Del Carpio, E. Ichiishi, N. Marze, D. Kuroda, S. S. r. Burman, J. J. Gray, E. Chermak, L. Cavallo, R. Oliva, A. Tovchigrechko, S. J. Wodak.
  
  Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment, in: Proteins - Structure, Function and Bioinformatics, February 2016. [ DOI : 10.1002/prot.25007 ]
  
  https://hal.inria.fr/hal-01309105
• 15M. 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, n^o 11, pp. 811 - 830. [ DOI : 10.4236/aim.2016.611079 ]
  
  https://hal.inria.fr/hal-01392860
• 16E. Neveu, D. Ritchie, P. Popov, S. Grudinin.
  
  PEPSI-Dock: a detailed data-driven protein–protein interaction potential accelerated by polar Fourier correlation, in: Bioinformatics, September 2016. [ DOI : 10.1093/bioinformatics/btw443 ]
  
  https://hal.archives-ouvertes.fr/hal-01358645
• 17D. Padhorny, A. Kazennov, B. S. Zerbe, K. A. Porter, B. Xia, S. Mottarella, Y. Kholodov, D. Ritchie, S. Vajda, D. Kozakov.
  
  Protein–protein docking by fast generalized Fourier transforms on 5D rotational manifolds, in: PNAS Early Edition, May 2016, vol. 113, n^o 30, pp. E4286-E4293. [ DOI : 10.1073/pnas.1603929113 ]
  
  https://hal.inria.fr/hal-01371087
• 18M. Richard, A. Chateau, C. Jelsch, C. Didierjean, X. Manival, C. Charron, B. Maigret, M. Barberi-Heyob, Y. Chapleur, C. Boura, N. Pellegrini-Moïse.
  
  Carbohydrate-based peptidomimetics targeting neuropilin-1: synthesis, molecular docking study and in vitro biological activities, in: Bioorganic and Medicinal Chemistry, November 2016, vol. 24, n^o 21, pp. 5315-5325. [ DOI : 10.1016/j.bmc.2016.08.052 ]
  
  https://hal.archives-ouvertes.fr/hal-01360034
• 19D. 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, n^o 1, pp. 158-167. [ DOI : 10.1107/S1600576715022931 ]
  
  https://hal.inria.fr/hal-01261402
• 20D. Ritchie.
  
  Calculating and scoring high quality multiple flexible protein structure alignments, in: Bioinformatics, May 2016, vol. 32, n^o 17, pp. 2650-2658. [ DOI : 10.1093/bioinformatics/btw300 ]
  
  https://hal.inria.fr/hal-01371083
• 21H. 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 ]
  
  https://hal.inria.fr/hal-01392842

Articles in Non Peer-Reviewed Journals

• 22M.-D. Devignes, M. Smaïl-Tabbone, D. Ritchie.
  
  Kbdock - Searching and organising the structural space of protein-protein interactions, in: ERCIM News, January 2016, n^o 104, pp. 24-25.
  
  https://hal.inria.fr/hal-01258117

International Conferences with Proceedings

• 23C. Chamard-Jovenin, A. Chesnel, E. Bresso, C. Morel, C. Thiébaut, M. Smaïl-Tabbone, E.-H. Djermoune, M.-D. Devignes, T. Boukhobza, H. Dumond.
  
  Transgenerational effects of ERalpha36 over-expression on mammary gland development and molecular phenotype: clinical perspective for breast cancer risk and therapy, in: 21st World Congress on Advances in Oncology and 19th International Symposium on Molecular Medicine, Athens, Greece, October 2016.
  
  https://hal.archives-ouvertes.fr/hal-01416469
• 24C. Chamard-Jovenin, A. Chesnel, C. Morel, M.-D. Devignes, M. Smaïl-Tabbone, T. Boukhobza, H. Dumond.
  
  Long chain alkylphenol mixture promotes breast cancer initiation and progression through an ERα36-mediated mechanism, in: 2nd French Workshop on Endocrine disruption in wildlife and human health, Paris, France, January 2016, Présentation Poster.
  
  https://hal.archives-ouvertes.fr/hal-01320688
• 25K. 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.
  
  https://hal.inria.fr/hal-01399232

National Conferences with Proceedings

• 26G. 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.
  
  https://hal.inria.fr/hal-01391172

Conferences without Proceedings

• 27G. 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.
  
  https://hal.inria.fr/hal-01369448

Scientific Books (or Scientific Book chapters)

• 28A. W. Ghoorah, M.-D. Devignes, M. Smaïl-Tabbone, D. Ritchie.
  
  Classification and Exploration of 3D Protein Domain Interactions Using Kbdock, in: Data Mining Techniques for the Life Sciences, O. Carugo, F. Eisenhaber (editors), Methods in Molecular Biology, Springer Science+Business Media New York, 2016, vol. 1415, pp. 91-105. [ DOI : 10.1007/978-1-4939-3572-7_5 ]
  
  https://hal.inria.fr/hal-01317448

References in notes

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  EC-PSI: Associating Enzyme Commission Numbers with Pfam Domains, in: JOBIM 2015, Clermont-Ferrand, France, July 2015. [ DOI : 10.1101/022343 ]
  
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• 35T. Bourquard, F. Landomiel, E. Reiter, P. Crépieux, D. W. Ritchie, J. Azé, A. Poupon.
  
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• 36M.-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, n^o 3/4, pp. 245-260.
  
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• 40W. J. Frawley, G. Piatetsky-Shapiro, C. J. Matheus.
  
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• 41R. 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.
• 42R. Gerbier, V. Leroux, P. Couvineau, R. Alvear-Perez, B. Maigret, C. Llorens-Cortes, X. Iturrioz.
  
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• 46H. I. Ingólfsson, C. A. Lopez, J. J. Uusitalo, D. H. de jong, S. M. Gopal, X. Periole, S. R. Marrink.
  
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• 49M. F. Lensink, S. J. Wodak.
  
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• 50L. 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.
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  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.
• 52I. H. Moal, P. A. Bates.
  
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• 53C. Morris.
  
  Towards a structural biology work bench, in: Acta Crystallographica, 2013, vol. PD69, pp. 681–682.
• 54D. 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
• 55S. 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.
  
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• 56G. 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
• 57G. 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.
  
  https://hal.inria.fr/hal-01095591
• 58B. Pierce, W. Tong, Z. Weng.
  
  M-ZDOCK: A Grid-Based Approach for $C_n$ Symmetric Multimer Docking, in: Bioinformatics, 2005, vol. 21, n^o 8, pp. 1472–1478.
• 59D. Ritchie, A. Ghoorah, L. Mavridis, V. Venkatraman.
  
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• 60D. Ritchie, G. J. Kemp.
  
  Protein docking using spherical polar Fourier correlations, in: Proteins: Structure, Function, and Genetics, 2000, vol. 39, pp. 178-194.
  
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• 61D. 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, n^o 17, pp. 1865-1873. [ DOI : 10.1093/bioinformatics/btn334 ]
  
  https://hal.inria.fr/inria-00434264
• 62D. Ritchie.
  
  Recent Progress and Future Directions in Protein-Protein Docking, in: Current Protein and Peptide Science, February 2008, vol. 9, n^o 1, pp. 1-15. [ DOI : 10.2174/138920308783565741 ]
  
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• 63A. 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.
  
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  Geometry-based flexible and symmetric protein docking, in: Proteins, 2005, vol. 60, n^o 2, pp. 224–231.
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• 72A. Özgur, Z. Xiang, D. R. Radev, Y. He.
  
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