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

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