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Bibliography

Publications of the year

Articles in International Peer-Reviewed Journals

  • 1M. 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 ]
    https://hal.inria.fr/hal-01388654
  • 2S. Grudinin, M. Garkavenko, A. Kazennov.
    Pepsi-SAXS : an adaptive method for rapid and accurate computation of small-angle X-ray scattering profiles, in: Acta Crystallographica Section D: Biological Crystallography, May 2017, vol. D73, pp. 449 - 464. [ DOI : 10.1107/S2059798317005745 ]
    https://hal.inria.fr/hal-01516719
  • 3I. Y. Gushchin, I. I. Melkinov, V. Polovinkin, A. Ishchenko, A. Yuzhakova, P. Buslaev, G. Bourenkov, S. Grudinin, E. Round, T. Balandin, V. Borshchevskiy, D. Willbold, G. Leonard, G. Büldt, A. Popov, V. I. Gordeliy.
    Mechanism of transmembrane signaling by sensor histidine kinases, in: Science, June 2017, vol. 356, no 6342, eaah6345 p. [ DOI : 10.1126/science.aah6345 ]
    https://hal.archives-ouvertes.fr/hal-01526454
  • 4A. Hoffmann, S. Grudinin.
    NOLB: Nonlinear Rigid Block Normal Mode Analysis Method, in: Journal of Chemical Theory and Computation, April 2017, vol. 13, no 5, pp. 2123-2134. [ DOI : 10.1021/acs.jctc.7b00197 ]
    https://hal.inria.fr/hal-01505843
  • 5A. Hoffmann, V. Perrier, S. Grudinin.
    A novel fast Fourier transform accelerated off-grid exhaustive search method for cryo-electron microscopy fitting, in: Journal of Applied Crystallography, August 2017, vol. 50, no 4, pp. 1036-1047. [ DOI : 10.1107/S1600576717008172 ]
    https://hal.inria.fr/hal-01553293
  • 6A. Ishchenko, E. Round, V. Borshchevskiy, S. Grudinin, I. Y. Gushchin, J. Klare, A. Remeeva, V. Polovinkin, P. Utrobin, T. Balandin, M. Engelhard, G. Büldt, V. I. Gordeliy.
    New Insights on Signal Propagation by Sensory Rhodopsin II/Transducer Complex, in: Scientific Reports, February 2017, vol. 7, 41811 p. [ DOI : 10.1038/srep41811 ]
    https://hal.inria.fr/hal-01458744
  • 7L. Jaillet, S. Artemova, S. Redon.
    IM-UFF: Extending the universal force field for interactive molecular modeling, in: Journal of Molecular Graphics and Modelling, October 2017, vol. 77, pp. 350 - 362. [ DOI : 10.1016/j.jmgm.2017.08.023 ]
    https://hal.inria.fr/hal-01676519
  • 8M. Kadukova, S. Grudinin.
    Convex-PL: a novel knowledge-based potential for protein-ligand interactions deduced from structural databases using convex optimization, in: Journal of Computer-Aided Molecular Design, October 2017, vol. 31, no 10, pp. 943–958. [ DOI : 10.1007/s10822-017-0068-8 ]
    https://hal.inria.fr/hal-01591154
  • 9M. Kadukova, S. Grudinin.
    Docking of small molecules to farnesoid X receptors using AutoDock Vina with the Convex-PL potential: lessons learned from D3R Grand Challenge 2, in: Journal of Computer-Aided Molecular Design, October 2017. [ DOI : 10.1007/s10822-017-0062-1 ]
    https://hal.inria.fr/hal-01591157
  • 10P.-L. Manteaux, C. Wojtan, R. Narain, S. Redon, F. Faure, M.-P. Cani.
    Adaptive Physically Based Models in Computer Graphics, in: Computer Graphics Forum, September 2017, vol. 36, no 6, pp. 312–337. [ DOI : 10.1111/cgf.12941 ]
    https://hal.inria.fr/hal-01367170
  • 11M. K. Nguyen, L. Jaillet, S. Redon.
    As-Rigid-As-Possible molecular interpolation paths, in: Journal of Computer-Aided Molecular Design, April 2017, vol. 31, no 4, pp. 403 - 417. [ DOI : 10.1007/s10822-017-0012-y ]
    https://hal.inria.fr/hal-01676132
  • 12K. K. Singh, S. Redon.
    Adaptively Restrained Molecular Dynamics in LAMMPS, in: Modelling and Simulation in Materials Science and Engineering, June 2017, vol. 25, no 5, 055013 p. [ DOI : 10.1088/1361-651X/aa7345 ]
    https://hal.archives-ouvertes.fr/hal-01525253
  • 13K. K. Singh, S. Redon.
    Single-pass Incremental Force Updates for Adaptively Restrained Molecular Dynamics, in: Journal of Computational Chemistry, December 2017. [ DOI : 10.1002/jcc.25126 ]
    https://hal.inria.fr/hal-01635863

International Conferences with Proceedings

  • 14K. K. Singh, D. F. Marin, S. Redon.
    Parallel Adaptively Restrained Molecular Dynamics, in: 2017 International Conference on High Performance Computing & Simulation (HPCS), Genova, Italy, IEEE, July 2017, pp. 308 - 314. [ DOI : 10.1109/HPCS.2017.55 ]
    https://hal.inria.fr/hal-01591466

Other Publications

References in notes
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    Application of Keating's valence force field model to non-ideal wurtzite materials, in: Physica E: Low-dimensional Systems and Nanostructures, 2010, vol. 42, no 5, pp. 1361–1364.
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    Long-time averaging for integrable Hamiltonian dynamics, in: Numerische Mathematik, 2005, vol. 100, pp. 211-232, 10.1007/s00211-005-0599-0.
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    Applications and implications of nanotechnologies for the food sector, in: Food Additives & Contaminants: Part A, 2008, vol. 25, no 3, pp. 241-258.
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  • 33X. Chen, S. S. Mao.
    Titanium Dioxide Nanomaterials: Synthesis, Properties, Modifications, and Applications, in: ChemInform, 2007, vol. 38, no 41.
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    Emergence of nanomedical devices for the diagnosis and treatment of cancer: the journey from basic science to commercialization, in: International Journal of Technology Transfer and Commercialisation, 2008, vol. 7, no 4, pp. 290-307.
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    The Fast Multipole Method: Numerical Implementation, in: Journal of Computational Physics, 2000.
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    Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin, in: Science, 2011, vol. 332, no 6031, pp. 816-821. [ DOI : 10.1126/science.1202617 ]
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    Structure, properties and wear performance of nano-multilayered TiAlCrSiYN/TiAlCrN coatings during machining of Ni-based aerospace superalloys, in: Surface and Coatings Technology, 2010, vol. 204, pp. 3698 - 3706. [ DOI : 10.1016/j.surfcoat.2010.04.050 ]
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