Bibliography

Publications of the year

Articles in International Peer-Reviewed Journals

• 1M. Bosson, S. Grudinin, S. Redon.
  Block-Adaptive Quantum Mechanics: An Adaptive Divide-and-Conquer Approach to Interactive Quantum Chemistry, in: Journal of Computational Chemistry, March 2013, vol. 34, n^o 6, pp. 492-504. [ DOI : 10.1002/jcc.23157 ]
  http://hal.inria.fr/hal-00755521
• 2I. Y. Gushchin, V. I. Gordeliy, S. Grudinin.
  Two Distinct States of the HAMP Domain from Sensory Rhodopsin Transducer Observed in Unbiased Molecular Dynamics Simulations, in: PLoS ONE, July 2013, vol. 8, n^o 7. [ DOI : 10.1371/journal.pone.0066917 ]
  http://hal.inria.fr/hal-00881143
• 3A. Ishchenko, E. Round, V. Borshchevskiy, S. Grudinin, I. Y. Gushchin, J. P. Klare, T. Balandin, A. Remeeva, M. Engelhard, G. Büldt, V. I. Gordeliy.
  Ground state structure of D75N mutant of sensory rhodopsin II in complex with its cognate transducer, in: Journal of Photochemistry and Photobiology B: Biology, June 2013, vol. 123, pp. 55-58. [ DOI : 10.1016/j.jphotobiol.2013.03.008 ]
  http://hal.inria.fr/hal-00881553
• 4M. Lensink, I. Moal, P. Bates, P. Kastritis, A. Melquiond, E. Karaca, C. Schmitz, M. Van Dijk, A. 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, J. Mitchell, J. Wieting, E. Kanamori, Y. Tsuchiya, Y. Murakami, J. Sarmiento, D. Standley, M. Shirota, K. Kinoshita, H. Nakamura, M. Chavent, D. Ritchie, H. Park, D. Ritchie, J. Ko, H. Lee, C. Seok, Y. Shen, D. Kozakov, S. Vajda, P. Kundrotas, I. Vakser, B. Pierce, H. Hwang, T. Vreven, Z. Weng, I. Buch, E. Farkash, H. Wolfson, M. Zacharias, S. Qin, H.-X. Zhou, S.-Y. Huang, X. Zou, J. Wojdyla, C. Kleanthous, S. J. Wodak.
  Blind prediction of interfacial water positions in CAPRI, in: Proteins, October 2013. [ DOI : 10.1002/prot.24439 ]
  http://hal.inria.fr/hal-00880345
• 5R. Moretti, S. J. Fleishman, R. Agius, M. Torchala, P. A. Bates, P. L. Kastritis, J. P. G. L. M. Rodrigues, M. Trellet, A. M. J. J. Bonvin, M. Cui, M. Rooman, D. Gillis, Y. Dehouck, I. Moal, M. Romero-Durana, L. Pérez-Cano, C. Pallara, B. Jiménez-Garcí, J. Fernández-Recio, S. C. Flores, M. Pacella, K. Praneeth Kilambi, J. J. Gray, P. Popov, S. Grudinin, J. Esquivel-Rodríguez, D. Kihara, N. Zhao, D. Korkin, X. Zhu, O. N. A. Demerdash, J. Mitchell, E. Kanamori, Y. Tsuchiya, H. Nakamura, H. Lee, H. Park, C. Seok, J. Sarmiento, S. Liang, S. Teraguchi, D. M. Standley, H. Shimoyama, G. Terashi, M. Takeda-Shitaka, M. Iwadate, H. Umeyama, D. Beglov, D. R. Hall, D. Kozakov, S. Vajda, B. G. Pierce, H. Hwang, T. Vreven, Z. Weng, Y. Huang, H. Li, X. Yang, X. Ji, S. Liu, Y. Xiao, M. Zacharias, S. Qin, H.-X. Zhou, S.-Y. Huang, X. Zou, S. Velankar, J. Janin, S. J. Wodak, D. Baker.
  Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions, in: Proteins, August 2013, vol. 81, n^o 11, pp. 1980 - 1987. [ DOI : 10.1002/prot.24356 ]
  http://hal.inria.fr/hal-00905794
• 6P. Popov, D. Ritchie, S. Grudinin.
  DockTrina: Docking triangular protein trimers, in: Proteins: Structure, Function, and Genetics, January 2014, vol. 82, n^o 1, pp. 34-44. [ DOI : 10.1002/prot.24344 ]
  http://hal.inria.fr/hal-00880359

International Conferences with Proceedings

• 7P.-L. Manteaux, F. Faure, S. Redon, M.-P. Cani.
  Exploring the Use of Adaptively Restrained Particles for Graphics Simulations, in: VRIPHYS 2013 - 10th Workshop on Virtual Reality Interaction and Physical Simulation, Lille, France, Eurographics Association, September 2013.
  http://hal.inria.fr/hal-00914653

References in notes

• 8I. Al-Bluwi, T. Siméon, J. Cortés.
  Motion planning algorithms for molecular simulations: A survey, in: Computer Science Review, 2012, vol. 6, n^o 4, pp. 125 - 143. [ DOI : 10.1016/j.cosrev.2012.07.002 ]
  http://www.sciencedirect.com/science/article/pii/S157401371200024X
• 9F. H. Allen.
  The Cambridge Structural Database: a quarter of a million crystal structures and rising, in: Acta Crystallographica Section B, Jun 2002, vol. 58, n^o 3 Part 1, pp. 380–388.
  http://dx.doi.org/10.1107/S0108768102003890
• 10S. Artemova, S. Grudinin, S. Redon.
  A comparison of neighbor search algorithms for large rigid molecules, in: Journal of Computational Chemistry, 2011, vol. 32, n^o 13, pp. 2865–2877.
  http://dx.doi.org/10.1002/jcc.21868
• 11S. 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
• 12H. 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, n^o 1, pp. 235-242. [ DOI : 10.1093/nar/28.1.235 ]
  http://nar.oxfordjournals.org/content/28/1/235.abstract
• 13M. Bosson, S. Grudinin, X. Bouju, S. Redon.
  Interactive physically-based structural modeling of hydrocarbon systems, in: Journal of Computational Physics, 2012, vol. 231, n^o 6, pp. 2581 - 2598. [ DOI : 10.1016/j.jcp.2011.12.006 ]
  http://www.sciencedirect.com/science/article/pii/S0021999111007042
• 14V. 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, n^o 3, pp. 712–725.
  http://dx.doi.org/10.1002/prot.21123
• 15D. W. Ritchie, G. J. Kemp.
  Protein docking using spherical polar Fourier correlations, in: Proteins: Structure, Function, and Bioinformatics, 2000, vol. 39, n^o 2, pp. 178–194.
  http://dx.doi.org/10.1002/(SICI)1097-0134(20000501)39:2<178::AID-PROT8>3.0.CO;2-6
• 16R. 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, n^o 13. [ DOI : 10.1093/bioinformatics/btm191 ]
  http://bioinformatics.oxfordjournals.org/content/23/13/i408.abstract