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Bibliography

Publications of the year

Articles in International Peer-Reviewed Journals

  • 1G. Derevyanko, S. Grudinin.
    HermiteFit: fast-fitting atomic structures into a low-resolution density map using three-dimensional orthogonal Hermite functions, in: Acta Crystallographica Section D: Biological Crystallography, August 2014, vol. 70, no 8, pp. 2069-2084. [ DOI : 10.1107/S1399004714011493 ]
    https://hal.inria.fr/hal-01078550
  • 2M. Dreher, J. Prevoteau-Jonquet, M. Trellet, M. Piuzzi, M. Baaden, B. Raffin, N. Férey, S. Robert, S. Limet.
    ExaViz: a Flexible Framework to Analyse, Steer and Interact with Molecular Dynamics Simulations, in: Faraday Discussions of the Chemical Society, May 2014, vol. 169, pp. 119-142. [ DOI : 10.1039/C3FD00142C ]
    https://hal.inria.fr/hal-00942627
  • 3M. P. Haag, A. C. Vaucher, M. Bosson, S. Redon, M. Reiher.
    Interactive Chemical Reactivity Exploration, in: ChemPhysChem, September 2014, vol. 15, no 15, pp. 3301–3319. [ DOI : 10.1002/cphc.201402342 ]
    https://hal.inria.fr/hal-01091971
  • 4I. Kufareva, V. Katritch, S. Grudinin, R. C. Stevens, R. Abagyan.
    Advances in GPCR Modeling Evaluated by the GPCR Dock 2013 Assessment: Meeting New Challenges, in: Structure, August 2014, vol. 22, no 8, pp. 1120–1139. [ DOI : 10.1016/j.str.2014.06.012 ]
    https://hal.inria.fr/hal-01078660
  • 5M. F. Lensink, A. H. Moal, P. A. Bates, L. Kastritis, S. J. Melquiond, E. Karaca, C. Schmitz, M. Van Dijk, M. J. J. Bonvin, M. Eisenstein, B. Jiménez-Garcí, S. Grosdidier, A. Solernou, L. Pérez-Cano, C. Pallar, J. Fernández-Recio, J. Xu, P. Muthu, K. Praneeth Kilambi, J. Gray, S. Grudinin, G. Derevyanko, C. Mitchell, J. Wieting, E. Kanamori, Y. Tsuchiya, Y. Murakami, J. Sarmiento, M. Standley, M. Shirota, K. Kinoshita, H. Nakamura, M. Chavent, D. Ritchie, H. Park, J. Ko, H. Lee, C. Seok, Y. Shen, D. Kozakov, S. Vajda, J. Kundrotas, A. Vakser, G. Pierce, H. Hwang, T. Vreven, Z. Weng, I. Buch, E. Farkash, J. Wolfson, M. Zacharias, S. Qin, H.-X. Zhou, S.-Y. Huang, X. Zou, A. Wojdyla, C. Kleanthous, J. Wodak.
    Blind prediction of interfacial water positions in CAPRI, in: Proteins, April 2014, vol. 82, no 4, pp. 620-632. [ DOI : 10.1002/prot.24439 ]
    https://hal.inria.fr/hal-00880345
  • 6P. Nogly, I. Y. Gushchin, A. Remeeva, A. M. Esteves, N. Borges, P. Ma, A. Ishchenko, S. Grudinin, E. Round, I. Moraes, V. Borshchevskiy, H. Santos, V. I. Gordeliy, M. Archer.
    X-ray structure of a CDP-alcohol phosphatidyltransferase membrane enzyme and insights into its catalytic mechanism, in: Nature Communications, June 2014, vol. 5. [ DOI : 10.1038/ncomms5169 ]
    https://hal.inria.fr/hal-01018657
  • 7P. Popov, S. Grudinin.
    Rapid determination of RMSDs corresponding to macromolecular rigid body motions, in: Journal of Computational Chemistry, May 2014, vol. 35, no 12, pp. 950-956. [ DOI : 10.1002/jcc.23569 ]
    https://hal.archives-ouvertes.fr/hal-00952248
  • 8P. Popov, D. Ritchie, S. Grudinin.
    DockTrina: Docking triangular protein trimers, in: Proteins: Structure, Function, and Genetics, January 2014, vol. 82, no 1, pp. 34-44. [ DOI : 10.1002/prot.24344 ]
    https://hal.inria.fr/hal-00880359
  • 9I. Sutkeviciute, M. Thépaut, S. Sattin, A. Berzi, J. Mcgeagh, S. Grudinin, J. Weiser, A. Le Roy, J. J. Reina, J. Rojo, M. Clerici, A. Bernadi, C. Ebel, F. Fieschi.
    Unique DC-SIGN Clustering Activity of a Small Glycomimetic: A Lesson for Ligand Design, in: ACS Chemical Biology, April 2014, vol. 9, no 6, pp. 1377-1385. [ DOI : 10.1021/cb500054h ]
    https://hal.inria.fr/hal-01018565

Scientific Books (or Scientific Book chapters)

  • 10S. Redon.
    Modélisation et simulation adaptatives pour les nanosciences, in: Modéliser & simuler. Epistémologies et pratiques de la modélisation et de la simulation, F. Varenne, M. Silberstein (editors), Éditions Matériologiques, November 2014, vol. 2.
    https://hal.inria.fr/hal-01085275
References in notes
  • 11M. A. Addicoat, N. Vankova, I. F. Akter, T. Heine.
    Extension of the Universal Force Field to Metal–Organic Frameworks, in: Journal of Chemical Theory and Computation, 2014, vol. 10, no 2, pp. 880–891.
  • 12I. Al-Bluwi, T. Siméon, J. Cortés.
    Motion planning algorithms for molecular simulations: A survey, in: Computer Science Review, 2012, vol. 6, no 4, pp. 125–143.
  • 13F. H. Allen.
    The Cambridge Structural Database: a quarter of a million crystal structures and rising, in: Acta Crystallographica Section B, Jun 2002, vol. 58, no 3 Part 1, pp. 380–388.
    http://dx.doi.org/10.1107/S0108768102003890
  • 14S. Artemova, S. Grudinin, S. Redon.
    A comparison of neighbor search algorithms for large rigid molecules, in: Journal of Computational Chemistry, 2011, vol. 32, no 13, pp. 2865–2877.
    http://dx.doi.org/10.1002/jcc.21868
  • 15S. Artemova, S. Redon.
    Adaptively Restrained Particle Simulations, in: Phys. Rev. Lett., Nov 2012, vol. 109.
    http://link.aps.org/doi/10.1103/PhysRevLett.109.190201
  • 16H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, P. E. Bourne.
    The Protein Data Bank, in: Nucleic Acids Research, 2000, vol. 28, no 1, pp. 235-242. [ DOI : 10.1093/nar/28.1.235 ]
    http://nar.oxfordjournals.org/content/28/1/235.abstract
  • 17M. Bosson, S. Grudinin, X. Bouju, S. Redon.
    Interactive physically-based structural modeling of hydrocarbon systems, in: Journal of Computational Physics, 2012, vol. 231, no 6, pp. 2581 - 2598. [ DOI : 10.1016/j.jcp.2011.12.006 ]
    http://www.sciencedirect.com/science/article/pii/S0021999111007042
  • 18V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg, C. Simmerling.
    Comparison of multiple Amber force fields and development of improved protein backbone parameters, in: Proteins: Structure, Function, and Bioinformatics, 2006, vol. 65, no 3, pp. 712–725.
    http://dx.doi.org/10.1002/prot.21123
  • 19A. K. Rappé, C. J. Casewit, K. Colwell, W. Goddard Iii, W. Skiff.
    UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations, in: Journal of the American Chemical Society, 1992, vol. 114, no 25, pp. 10024–10035.
  • 20D. W. Ritchie, G. J. Kemp.
    Protein docking using spherical polar Fourier correlations, in: Proteins: Structure, Function, and Bioinformatics, 2000, vol. 39, no 2, pp. 178–194.
    http://dx.doi.org/10.1002/(SICI)1097-0134(20000501)39:2<178::AID-PROT8>3.0.CO;2-6
  • 21D. Ritchie, D. Kozakov, S. Vajda.
    Accelerating and Focusing Protein-Protein Docking Correlations Using Multi-Dimensional Rotational FFT Generating Functions, in: Bioinformatics, 2008, vol. 24, pp. 1865-1873.
  • 22R. Rossi, M. Isorce, S. Morin, J. Flocard, K. Arumugam, S. Crouzy, M. Vivaudou, S. Redon.
    Adaptive torsion-angle quasi-statics: a general simulation method with applications to protein structure analysis and design, in: Bioinformatics, 2007, vol. 23, no 13. [ DOI : 10.1093/bioinformatics/btm191 ]
    http://bioinformatics.oxfordjournals.org/content/23/13/i408.abstract

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