S. K. Card, J. D. Mackinlay, and B. Shneiderman, Readings in Information Visualization: Using Vision to Think, 1999.

T. Munzner, Visualization Analysis and Design, A K Peters, 2014.

C. Ware, Information Visualization: Perception for Design, 2012.

A. C. Telea, Data Visualization: Principles and Practice, A K Peters, 2014.

J. S. Richardson, Schematic drawings of protein structures, in: Diffraction Methods for Biological Macromolecules Part B, vol.115, pp.15026-15029, 1985.

C. L. Bajaj, V. Pascucci, A. Shamir, R. J. Holt, and A. N. Netravali, Dynamic maintenance and visualization of molecular surfaces, Discrete Applied Mathematics, vol.127, issue.1, pp.23-51, 2003.

B. Alberts, A. Johnson, J. Lewis, D. Morgan, M. Raff et al., Molecular Biology of the Cell, 2014.

M. Erwig, K. Smeltzer, and X. Wang, What is a visual language?, Journal of Visual Languages & Computing, vol.38, pp.9-17, 2017.

T. Walsum and F. H. Post, Selective visualization of vector fields, Computer Graphics Forum, vol.13, issue.3, pp.339-347, 1994.

D. Ceneda, T. Gschwandtner, T. May, S. Miksch, H. Schulz et al., Tominski, Characterizing guidance in visual analytics, IEEE Transactions on Visualization and Computer Graphics, vol.23, issue.1, pp.111-120, 2017.

A. Cockburn, A. Karlson, and B. B. Bederson, A review of overview+detail, zooming, and focus+context interfaces, ACM Computing Surveys, vol.41, issue.1, p.31, 2009.

H. Hauser, Scientific Visualization: The Visual Extraction of Knowledge from Data, pp.305-327, 2005.

D. Albers, M. Correll, and M. Gleicher, Task-driven evaluation of aggregation in time series visualization, Proceedings of the SIGCHI Conference on Human Factors in Computing Systems, pp.551-560, 2014.

J. Kreiser, M. Meuschke, G. Mistelbauer, B. Preim, and T. Ropinski, A survey of flattening-based medical visualization techniques, Computer Graphics Forum, vol.37, issue.3, pp.597-624, 2018.

R. A. Becker and W. S. Cleveland, Brushing scatterplots, Technometrics, vol.29, issue.2, pp.127-142, 1987.

A. Buja, J. A. Mcdonald, J. Michalak, and W. Stuetzle, Interactive data visualization using focusing and linking, Proc. Visualization, pp.156-163, 1991.

G. Wills, Handbook of Data Visualization, pp.217-241, 2008.

P. A. Craig, L. V. Michel, and R. C. Bateman, A survey of educational uses of molecular visualization freeware, Biochemistry and Molecular Biology Education, vol.41, issue.3, pp.193-205, 2013.

N. Elmqvist and P. Tsigas, A taxonomy of 3d occlusion management for visualization, IEEE Transactions on Visualization and Computer Graphics, vol.14, issue.5, pp.1095-1109, 2008.

A. Mahdavi-amiri, T. Alderson, and F. Samavati, A survey of digital earth, Computers & Graphics, vol.53, pp.95-117, 2015.

H. Schumann and W. Müller, Visualisierung: Grundlagen und allgemeine Methoden, 2000.

I. Viola and T. Isenberg, Pondering the concept of abstraction in (illustrative) visualization, IEEE Transactions on Visualization and Computer Graphics, vol.24, issue.9, pp.2573-2588, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01581177

M. Mittring, Finding next gen: Cryengine 2, ACM SIGGRAPH 2007 Courses, SIGGRAPH '07, pp.97-121, 2007.

M. L. Muzic, M. Waldner, J. Parulek, and I. Viola, Illustrative timelapse: A technique for illustrative visualization of particle-based simulations, Proc. IEEE Pacific Visualization Symposium (PacificVis), pp.247-254, 2015.

G. W. Furnas and B. B. Bederson, Space-scale diagrams: Understanding multiscale interfaces, Proceedings of the SIGCHI Conference on Human Factors in Computing Systems, pp.234-241, 1995.

M. Karplus and J. A. Mccammon, Molecular dynamics simulations of biomolecules, Nature Structural & Molecular Biology, vol.9, issue.9, pp.902-646, 2002.

M. Karplus, Molecular dynamics of biological macromolecules: A brief history and perspective, Biopolymers, vol.68, issue.3, pp.350-358, 2003.
DOI : 10.1002/bip.10266

U. Hensen, T. Meyer, J. Haas, R. Rex, G. Vriend et al., Exploring protein dynamics space: The dynasome as the missing link between protein structure and function, PLoS ONE, vol.7, issue.5, pp.1-16, 2012.
DOI : 10.1371/journal.pone.0033931
URL : https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0033931&type=printable

G. Zhao, J. R. Perilla, E. L. Yufenyuy, X. Meng, B. Chen et al., Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics, Nature, vol.497, issue.7451, pp.643-646, 2013.
DOI : 10.1038/nature12162
URL : http://europepmc.org/articles/pmc3729984?pdf=render

M. Baram, Y. Atsmon-raz, B. Ma, R. Nussinov, and Y. Miller, Amylin-A? oligomers at atomic resolution using molecular dynamics simulations: A link between Type 2 diabetes and Alzheimer's disease, Physical Chemistry Chemical Physics, vol.18, issue.4, pp.2330-2338, 2016.
DOI : 10.1039/c5cp03338a
URL : http://pubs.rsc.org/en/content/articlepdf/2016/cp/c5cp03338a

F. Noe, Beating the millisecond barrier in molecular dynamics simulations, Biophysical Journal, vol.108, issue.2, pp.228-229, 2015.

M. Krone, B. Kozlíková, N. Lindow, M. Baaden, D. Baum et al., Visual analysis of biomolecular cavities: State of the art, Computer Graphics Forum, vol.35, issue.3, pp.527-551, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01400464

N. Prabhu and K. Sharp, Protein-solvent interactions, Chemical Reviews, vol.106, issue.5, pp.1616-1623, 2006.

S. Huang, Search strategies and evaluation in protein-protein docking: Principles, advances and challenges, Drug Discovery Today, vol.19, issue.8, pp.1081-1096, 2014.
DOI : 10.1016/j.drudis.2014.02.005

B. Tversky, J. B. Morrison, and M. Betrancourt, Animation: Can it facilitate?, International Journal of Human-Computer Studies, vol.57, issue.4, pp.247-262, 2002.

B. Kozlíková, M. Krone, M. Falk, N. Lindow, M. Baaden et al., Visualization of biomolecular structures: State of the art revisited, vol.36, pp.178-204, 2017.

K. Furmanová, M. Jare?ová, J. By?ka, A. Jur?ík, J. Parulek et al., Interactive exploration of ligand transportation through protein tunnels, BMC Bioinformatics, vol.18, pp.1-16, 2017.

V. Vad, J. By?ka, A. Jur?ík, I. Viola, E. Gröller et al., Watergate: Visual exploration of water trajectories in protein dynamics, Proc. Eurographics Workshop on Visual Computing for Biology and Medicine, The Eurographics Association, pp.33-42, 2017.

J. By?ka, A. Jur?ik, M. E. Gröller, I. Viola, and B. Kozlíková, MoleCollar and Tunnel Heat Map visualizations for conveying spatio-temporo-chemical properties across and along protein voids, Computer Graphics Forum, vol.34, issue.3, 2015.

J. By?ka, M. L. Muzic, M. E. Gröller, I. Viola, and B. Kozlíková, AnimoAminoMiner: Exploration of protein tunnels and their properties in molecular dynamics, IEEE Transactions on Visualization and Computer Graphics, vol.22, issue.1, pp.747-756, 2016.

M. Krone, G. Reina, C. Schulz, T. Kulschewski, J. Pleiss et al., Interactive extraction and tracking of biomolecular surface features, Computer Graphics Forum, vol.32, issue.3, pp.331-340, 2013.
DOI : 10.1111/cgf.12120

S. Zhukov, A. Iones, and G. Kronin, An ambient light illumination model, Rendering Techniques'98, pp.45-56, 1998.
DOI : 10.1007/978-3-7091-6453-2_5

P. W. Rothemund, Folding DNA to create nanoscale shapes and patterns, Nature, vol.440, issue.7082, pp.297-302, 2006.
DOI : 10.1038/nature04586
URL : https://authors.library.caltech.edu/22244/2/nature04586-s1.pdf

H. Miao, E. De-llano, J. Sorger, Y. Ahmadi, T. Kekic et al., Multiscale visualization and scale-adaptive modification of DNA nanostructures, IEEE Transactions on Visualization and Computer Graphics, vol.24, issue.1, pp.1014-1024, 2018.
DOI : 10.1109/tvcg.2017.2743981
URL : https://hal.archives-ouvertes.fr/hal-01581203

H. Miao, E. De-llano, T. Isenberg, M. E. Gröller, I. Bari?i´bari?i´c et al., DimSUM: Dimension and scale unifying map for visual abstraction of DNA origami structures, Computer Graphics Forum, vol.37, issue.3, pp.403-413, 2018.
DOI : 10.1111/cgf.13429

S. M. Douglas, A. H. Marblestone, S. Teerapittayanon, A. Vazquez, G. M. Church et al., Rapid prototyping of 3D DNA-origami shapes with caDNAno, Nucleic Acids Research, vol.37, issue.15, pp.5001-5006, 2009.
DOI : 10.1093/nar/gkp436
URL : https://academic.oup.com/nar/article-pdf/37/15/5001/16752788/gkp436.pdf

W. Humphrey, A. Dalke, and K. Schulten, VMD: Visual molecular dynamics, Journal of Molecular Graphics, vol.14, issue.1, pp.33-38, 1996.

, Schrödinger release 2017-1: Maestro, Schrödinger, LLC, 2017.

W. Lueks, I. Viola, M. Van-der-zwan, H. Bekker, and T. Isenberg, Spatially continuous change of abstraction in molecular visualization, Abstracts of BioVis, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00781520

M. Van-der-zwan, W. Lueks, H. Bekker, and T. Isenberg, Illustrative molecular visualization with continuous abstraction, Computer Graphics Forum, vol.30, issue.3, pp.683-690, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00781508

H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat et al., The protein data bank, Nucleic Acids Research, vol.28, issue.1, pp.235-242, 2000.

G. T. Johnson, L. Autin, M. Al-alusi, D. S. Goodsell, M. F. Sanner et al., cellPACK: A virtual mesoscope to model and visualize structural systems biology, Nature Methods, vol.12, issue.1, pp.85-91, 2015.

P. Shirley, M. Ashikhmin, and S. Marschner, Fundamentals of Computer Graphics, 2010.

S. Oeltze-jafra and B. Preim, Survey of labeling techniques in medical visualizations, Proc. of VCBM, Eurographics Association, pp.199-208, 2014.

M. Tarini, P. Cignoni, and C. Montani, Ambient occlusion and edge cueing for enhancing real time molecular visualization, IEEE Transactions on Visualization and Computer Graphics, vol.12, issue.5, pp.1237-1244, 2006.

J. F. Blinn, A generalization of algebraic surface drawing, ACM Transactions on Graphics, vol.1, issue.3, pp.235-256, 1982.

C. Müller, S. Grottel, and T. Ertl, Image-space GPU metaballs for time-dependent particle data sets, Proceedings of VMV, Aka GmbH, pp.31-40, 2007.

W. Straßer, Schnelle Kurven-und Flächendarstellung auf grafischen Sichtgeräten, 1974.

N. Greene, M. Kass, and G. Miller, Hierarchical z-buffer visibility, Proc. SIGGRAPH, pp.231-238, 1993.

M. L. Muzic, L. Autin, J. Parulek, and I. Viola, cellVIEW: A tool for illustrative and multi-scale rendering of large biomolecular datasets, Proc. Eurographics Workshop on Visual Computing for Biology and Medicine, The Eurographics Association, pp.61-70, 2015.

T. Klein, L. Autin, B. Kozlíková, D. S. Goodsell, A. Olson et al., Instant construction and visualization of crowded biological environments, IEEE Transactions on Visualization and Computer Graphics, vol.24, issue.1, pp.862-872, 2018.

O. D. Lampe, I. Viola, N. Reuter, and H. Hauser, Two-level approach to efficient visualization of protein dynamics, IEEE Transactions on Visualization and Computer Graphics, vol.13, issue.6, pp.1616-1623, 2007.

M. L. Muzic, J. Parulek, A. Stavrum, and I. Viola, Illustrative visualization of molecular reactions using omniscient intelligence and passive agents, Computer Graphics Forum, vol.33, issue.3, pp.141-150, 2014.

M. L. Muzic, P. Mindek, J. Sorger, L. Autin, D. Goodsell et al., Visibility equalizer: Cutaway visualization of mesoscopic biological models, Computer Graphics Forum, vol.35, issue.3, pp.161-170, 2016.

N. Waldin, M. L. Muzic, M. Waldner, M. E. Gröller, D. Goodsell et al., Chameleon: Dynamic color mapping for multi-scale structural biology models, Proc. Eurographics Workshop on Visual Computing for Biology and Medicine, The Eurographics Association, pp.11-20, 2016.

K. Been, M. Nöllenburg, S. Poon, and A. Wolff, Optimizing active ranges for consistent dynamic map labeling, Computational Geometry, vol.43, issue.3, pp.312-328, 2010.

D. Kou?il, L. Cmolík, B. Kozlíková, H. Wu, G. Johnson et al., Labels on levels: Labeling of multi-scale multi-instance and crowded 3D biological environments, IEEE Transactions on Visualization and Computer Graphics, vol.25, issue.1

J. Mccrae, I. Mordatch, M. Glueck, and A. Khan, Multiscale 3D navigation, Proc. Symposium on Interactive 3D Graphics and Games, pp.7-14, 2009.

E. Axelsson, J. Costa, C. Silva, C. Emmart, A. Bock et al., Dynamic scene graph: Enabling scaling, positioning, and navigation in the universe, Computer Graphics Forum, vol.36, issue.3, pp.459-468, 2017.
DOI : 10.1111/cgf.13202

J. H. Clark, Hierarchical geometric models for visible surface algorithms, Communications of the ACM, vol.19, issue.10, pp.547-554, 1976.
DOI : 10.1145/965143.563323

W. Hsu, K. Ma, and C. Correa, A rendering framework for multiscale views of 3D models, ACM Transactions on Graphics, vol.30, issue.6, 2011.
DOI : 10.1145/2024156.2024165
URL : http://vis.cs.ucdavis.edu/papers/multiscaleRendering_sigA_11.pdf

T. Luft, C. Colditz, and O. Deussen, Image enhancement by unsharp masking the depth buffer, ACM Transactions on Graphics, vol.25, issue.3, pp.1206-1213, 2006.
DOI : 10.1145/1179352.1142016
URL : http://vision.ai.uiuc.edu/~tankh/citations/nonphotorealistic_camera_siggraph2004/luft_TOG2006.pdf

S. Grottel, M. Krone, K. Scharnowski, and T. Ertl, Object-space ambient occlusion for molecular dynamics, Proc. IEEE Pacific Visualization Symposium, pp.209-216, 2012.
DOI : 10.1109/pacificvis.2012.6183593

J. Parulek, T. Ropinski, and I. Viola, Seamless abstraction of molecular surfaces, Proc. Spring Conference on Computer Graphics, pp.107-114, 2013.
DOI : 10.1145/2508244.2508258
URL : http://www.cg.tuwien.ac.at/research/publications/2013/Viola_Ivan_2013_SVA/Viola_Ivan_2013_SVA-Paper.pdf

N. Lindow, D. Baum, and H. Hege, Interactive rendering of materials and biological structures on atomic and nanoscopic scale, Computer Graphics Forum, vol.31, issue.3pt4, pp.1325-1334, 2012.
DOI : 10.1111/j.1467-8659.2012.03128.x

J. Parulek, D. Jönsson, T. Ropinski, S. Bruckner, A. Ynnerman et al., Continuous levels-of-detail and visual abstraction for seamless molecular visualization, Computer Graphics Forum, vol.33, issue.6, pp.276-287, 2014.
DOI : 10.1111/cgf.12349
URL : http://onlinelibrary.wiley.com/doi/10.1111/cgf.12349/pdf

J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid et al., Scalable molecular dynamics with NAMD, vol.26, pp.1781-1802, 2005.
DOI : 10.1002/jcc.20289
URL : http://europepmc.org/articles/pmc2486339?pdf=render

S. Grottel, M. Krone, C. Müller, G. Reina, and T. Ertl, MegaMol-A prototyping framework for particle-based visualization, IEEE Transactions on Visualization and Computer Graphics, vol.21, issue.2, pp.201-214, 2015.
DOI : 10.1109/tvcg.2014.2350479

B. Kozlíková, E. Sebestová, V. Sustr, J. Brezovsk´ybrezovsk´y, O. Strnad et al., CAVER Analyst 1.0: Graphic tool for interactive visualization and analysis of tunnels and channels in protein structures, Bioinformatics, vol.30, issue.18, pp.2684-2685, 2014.

N. Inria and . Samson, Software for adaptive modeling and simulation of nanosystems, 2018.

, MARA-Molecular analytical robotics assays, 2018.

P. Mindek, D. Kou?il, J. Sorger, D. Toloudis, B. Lyons et al., Visualization multi-pipeline for communicating biology, IEEE Transactions on Visualization and Computer Graphics, vol.24, issue.1, pp.883-892, 2018.