C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid et al., Scalable molecular dynamics with NAMD, Journal of Computational Chemistry, vol.84, issue.16, pp.1781-1802, 2005.
DOI : 10.1002/jcc.20289

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2486339

C. Hess, D. Kutzner, E. Van-der-spoel, and . Lindahl, GROMACS 4:?? Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation, Journal of Chemical Theory and Computation, vol.4, issue.3, pp.435-447, 2008.
DOI : 10.1021/ct700301q

. Thomas, Illuminating the Path: The Research and Development Agenda for Visual Analytics, 2005.

B. Lindahl, D. Hess, . Van-der, and . Spoel, GROMACS 3.0: a package for molecular simulation and trajectory analysis, Journal of Molecular Modeling, vol.7, issue.8, pp.306-323, 2001.
DOI : 10.1007/s008940100045

D. Faraldo-gomez, G. R. Smith, and M. S. Sansom, Molecular Dynamics Simulations of the Bacterial Outer Membrane Protein FhuA: A Comparative Study of the Ferrichrome-Free and Bound States, Biophysical Journal, vol.85, issue.3, pp.1406-1426, 2003.
DOI : 10.1016/S0006-3495(03)74573-1

D. Faraldo-gomez, L. R. Forrest, M. Baaden, P. J. Bond, C. Domene et al., Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations, Proteins: Structure, Function, and Bioinformatics, vol.333, issue.4, pp.783-791, 2004.
DOI : 10.1002/prot.20257

E. Garcia and K. Y. Sanbonmatsu, ??-Helical stabilization by side chain shielding of backbone hydrogen bonds, Proceedings of the National Academy of Sciences, vol.99, issue.5, pp.2782-2787, 2002.
DOI : 10.1073/pnas.042496899

J. Allard, B. Lesage, and . Raffin, Modularity for Large Virtual Reality Applications, Presence: Teleoperators and Virtual Environments, vol.7, issue.1, pp.142-162, 2010.
DOI : 10.1016/S0167-8191(02)00189-8

URL : https://hal.archives-ouvertes.fr/hal-00688474

S. Pronk, R. Pall, P. Schulz, P. Larsson, R. Bjelkmar et al., GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit, Bioinformatics, vol.29, issue.7, pp.845-854, 2013.
DOI : 10.1093/bioinformatics/btt055

A. Humphrey, K. Dalke, and . Schulten, VMD: Visual molecular dynamics, Journal of Molecular Graphics, vol.14, issue.1, pp.33-38, 1996.
DOI : 10.1016/0263-7855(96)00018-5

E. J. Michaud-agrawal, T. B. Denning, O. Woolf, and . Beckstein, MDAnalysis: A toolkit for the analysis of molecular dynamics simulations, Journal of Computational Chemistry, vol.4, issue.Suppl. 2, pp.2319-2327, 2011.
DOI : 10.1002/jcc.21787

A. Chavent, A. Vanel, B. Tek, S. Levy, B. Robert et al., GPU-accelerated atom and dynamic bond visualization using hyperballs: A unified algorithm for balls, sticks, and hyperboloids, Journal of Computational Chemistry, vol.331, issue.Pt 5, pp.2924-2935, 2011.
DOI : 10.1002/jcc.21861

URL : https://hal.archives-ouvertes.fr/hal-00645162

D. J. Cruz-neira, T. A. Sandin, R. V. Defanti, J. C. Kenyon, and . Hart, The CAVE: audio visual experience automatic virtual environment, Communications of the ACM, vol.35, issue.6, pp.64-72, 1992.
DOI : 10.1145/129888.129892

S. Goodsell and A. J. Olson, Annual review of biophysics and biomolecular structure, pp.105-153, 2000.

E. Hanson, S. Wernert, and . Hughes, Scientific Visualization: Dagstuhl '97 Proceedings, IEEE Computer, pp.95-104, 1997.
DOI : 10.1007/978-1-4471-6497-5

S. J. Yesylevskyy, A. E. Marrink, and . Mark, Alternative Mechanisms for the Interaction of the Cell-Penetrating Peptides Penetratin and the TAT Peptide with Lipid Bilayers, Biophysical Journal, vol.97, issue.1, pp.40-49, 2009.
DOI : 10.1016/j.bpj.2009.03.059

K. Ludemann, V. Lounnas, and R. C. Wade, How do substrates enter and products exit the buried active site of cytochrome P450cam? 2. Steered molecular dynamics and adiabatic mapping of substrate pathways, Journal of Molecular Biology, vol.303, issue.5, pp.813-830, 2000.
DOI : 10.1006/jmbi.2000.4155

J. Marrink, H. J. Risselada, S. Yefimov, D. P. Tieleman, and A. H. De-vries, The MARTINI Force Field:?? Coarse Grained Model for Biomolecular Simulations, The Journal of Physical Chemistry B, vol.111, issue.27, pp.7812-7824, 2007.
DOI : 10.1021/jp071097f

K. Konyha, D. Matkovic, M. Gracanin, H. Jelovic, and . Hauser, Interactive Visual Analysis of Families of Function Graphs, IEEE Transactions on Visualization and Computer Graphics, vol.12, issue.6, pp.1373-1385, 2006.
DOI : 10.1109/TVCG.2006.99

A. Turkay, A. Lundervold, H. Lundervold, and . Hauser, Visualization and Computer Graphics, IEEE Transactions on, vol.18, pp.2621-2630, 2012.