Source: https://raweb.inria.fr/rapportsactivite/RA2017/capsid/bibliography.html
Timestamp: 2019-04-22 07:00:50+00:00

Document:
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.
T. Hoang, X. Cavin, P. Schultz, D. Ritchie.
G. Macindoe, L. Mavridis, V. Venkatraman, M.-D. Devignes, D. Ritchie.
V. Pérez-Nueno, A. S. Karaboga, M. Souchet, D. Ritchie.
D. W. Ritchie, S. Grudinin.
D. W. Ritchie, V. Venkatraman.
S. Z. Alborzi, M.-D. Devignes, D. W. Ritchie.
S. Aridhi, A. Montresor, Y. Velegrakis.
C. Coluzzi, G. Guédon, M.-D. Devignes, C. Ambroset, V. Loux, S. Payot, N. N. Leblond-Bourget, T. Lacroix.
S. Dey, D. Ritchie, E. D. Levy.
W. Dhifli, S. Aridhi, E. Mephu Nguifo.
M. El Houasli, B. Maigret, M.-D. Devignes, A. W. Ghoorah, S. Grudinin, D. Ritchie.
N. E. I. Karabadji, H. Seridi, F. Bousetouane, W. Dhifli, S. Aridhi.
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.
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, biofunctionprediction.org, July 2017.
S. Z. Alborzi, M.-D. Devignes, D. Ritchie.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Towards a structural biology work bench, in: Acta Crystallographica, 2013, vol. PD69, pp. 681–682.
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.
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.
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.
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.
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.
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.
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.
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.

References: V. 
 V. 

V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V.