The Definitive Guide to Programmable Real-Time Graphics, 2003. ,
Illustrative Visualization of Molecular Reactions using Omniscient Intelligence and Passive Agents, Computer Graphics Forum, vol.33, issue.3, pp.141-150, 2014. ,
Extending the graphic pipeline with new gpuaccelerated primitives, 2004. ,
GPU-based Ray-casting of Quadratic Surfaces, Proceedings of the 3rd Eurographics / IEEE VGTC Conference on Point-Based Graphics, pp.59-65, 2006. ,
GPU-accelerated atom and dynamic bond visualization using hyperballs: A unified algorithm for balls, sticks, and hyperboloids, Journal of Computational Chemistry, vol.32, issue.13, pp.2924-2935, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00645162
Computer-generated schematic diagrams of protein structures, Science, vol.216, issue.4545, pp.539-540, 1982. ,
Ribbons 2.0, Journal of Applied Crystallography, vol.24, issue.5, pp.958-961, 1991. ,
, YASARA -Yet Another Scientific Artificial Reality Application
,
A System for Interactive Molecular Dynamics Simulation, Proceedings of the 2001 Symposium on Interactive 3D Graphics, pp.191-194, 2001. ,
A coarse-grained protein force field for folding and structure prediction, Proteins, vol.69, issue.2, pp.394-408, 2007. ,
Replica-exchange molecular dynamics method for protein folding, Chemical Physics Letters, vol.314, issue.1, pp.141-151, 1999. ,
Coarse Grained Model for Semiquantitative Lipid Simulations, The Journal of Physical Chemistry B, vol.108, issue.2, pp.750-760, 2004. ,
Integrative computational modeling of protein interactions, FEBS Journal, vol.281, issue.8, pp.1988-2003, 2014. ,
Predicting protein structures with a multiplayer online game, Nature, issue.7307, pp.756-760, 2010. ,
Game on, science -how video game technology may help biologists tackle visualization challenges, PloS one, vol.8, issue.3, p.57990, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-01084644
From polypeptide sequences to structures using Monte Carlo simulations and an optimized potential, The Journal of Chemical Physics, vol.111, issue.5, pp.2301-2310, 1999. ,
HiRE-RNA: a high resolution coarse-grained energy model for RNA, The journal of physical chemistry. B, vol.114, issue.37, pp.11957-11966, 2010. ,
High performance molecular simulations through multi-level parallelism from laptops to supercomputers, SoftwareX, pp.1-2, 2015. ,
Scalable molecular dynamics with NAMD, Journal of Computational Chemistry, vol.26, issue.16, pp.1781-1802, 2005. ,
Two Crystal Structures of the B1 Immunoglobulin-Binding Domain of Streptococcal Protein G and Comparison with NMR, Biochemistry, vol.33, issue.15, pp.4721-4729, 1994. ,
Structured Computer Organization, 2005. ,
Physically Based Rendering, Third Edition: From Theory to Implementation, 2016. ,
, CRYENGINE | The complete solution for next generation game development by Crytek
,
, Unity. Unity -Scripting API: MonoBehaviour
Hierarchical Geometric Models for Visible Surface Algorithms, Commun. ACM, vol.19, issue.10, pp.547-554, 1976. ,
Two-Level Approach to Efficient Visualization of Protein Dynamics, IEEE Transactions on Visualization and Computer Graphics, vol.13, issue.6, pp.1616-1623, 2007. ,
The Machinery of Life, 2009. ,
Deformable Smooth Surface Design. Discrete & Computational Geometry, vol.21, pp.87-115, 1999. ,
MetaMol: High-quality visualization of molecular skin surface, Journal of Molecular Graphics and Modelling, vol.27, issue.2, pp.209-216, 2008. ,
URL : https://hal.archives-ouvertes.fr/inria-00339122
The structure of proteins; two hydrogenbonded helical configurations of the polypeptide chain, Proceedings of the National Academy of Sciences of the United States of America, vol.37, pp.205-211, 1951. ,
The discovery of the ?-helix and ?-sheet, the principal structural features of proteins, Proceedings of the National Academy of Sciences, vol.100, issue.20, pp.11207-11210, 2003. ,
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features, Biopolymers, vol.22, issue.12, pp.2577-2637, 1983. ,
Knowledge-based protein secondary structure assignment, Proteins: Structure, Function, and Bioinformatics, vol.23, issue.4, pp.566-579, 1995. ,
GPU-based Visualisation of Protein Secondary Structure. ResearchGate, pp.115-122, 2008. ,
ProteinShader: illustrative rendering of macromolecules, BMC Structural Biology, vol.9, p.19, 2009. ,
VMD: visual molecular dynamics, Journal of Molecular Graphics, vol.14, issue.1, pp.27-28, 1996. ,
, An Open-Source Molecular Graphics Tool
UCSF Chimera-a visualization system for exploratory research and analysis, Journal of Computational Chemistry, vol.25, issue.13, pp.1605-1612, 2004. ,
WebGL protein viewer, vol.18, p.28, 2017. ,
,
Pepsi-SAXS: an adaptive method for rapid and accurate computation of small-angle X-ray scattering profiles, Acta Crystallographica Section D: Structural Biology, vol.73, issue.5, pp.449-464, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01516719
, Tachyon Parallel / Multiprocessor Ray Tracing System
ExaViz: a flexible framework to analyse, steer and interact with molecular dynamics simulations, Faraday Discussions, vol.169, issue.0, pp.119-142, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-00942627
A Middleware for Large Scale Virtual Reality Applications. Euro-Par 2004 Parallel Processing, pp.497-505, 2004. ,
URL : https://hal.archives-ouvertes.fr/hal-00085302
X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation, Nature, vol.457, issue.7225, pp.111-114, 2009. ,
The Lit Sphere: A Model for Capturing NPR Shading from Art, Proceedings of Graphics Interface, pp.143-150, 2001. ,
Three-dimensional representations of complex carbohydrates and polysaccharides-SweetUnityMol: A video gamebased computer graphic software, Glycobiology, p.133, 2014. ,
Marching Cubes: A High Resolution 3d Surface Construction Algorithm, Proceedings of the 14th Annual Conference on Computer Graphics and Interactive Techniques, pp.163-169, 1987. ,
A simple method for displaying the hydropathic character of a protein, Journal of Molecular Biology, vol.157, issue.1, pp.105-132, 1982. ,
Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins, Annual Review of Biophysics and Biophysical Chemistry, vol.15, pp.321-353, 1986. ,
Analysis of membrane and surface protein sequences with the hydrophobic moment plot, Journal of Molecular Biology, vol.179, issue.1, pp.125-142, 1984. ,
Experimentally determined hydrophobicity scale for proteins at membrane interfaces, Nature Structural Biology, vol.3, issue.10, pp.842-848, 1996. ,
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. ,
Molecular dynamics: thermostats and barostatsThermostats_and_barostats ,
,
Advanced Computer Simulation, Advances in Polymer Science, pp.105-149 ,
,
, Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules. Physical Review, vol.159, issue.1, pp.98-103, 1967.
Molecular dynamics with coupling to an external bath, The Journal of Chemical Physics, vol.81, issue.8, pp.3684-3690, 1984. ,
Molecular dynamics simulations at constant pressure and/or temperature, The Journal of Chemical Physics, vol.72, issue.4, pp.2384-2393, 1980. ,
DOI : 10.1063/1.439486
Canonical dynamics: Equilibrium phase-space distributions, Physical Review A, vol.31, issue.3, pp.1695-1697, 1985. ,
DOI : 10.1103/physreva.31.1695
Interactive Molecular Dynamics: Scaling up to Large Systems, International Conference on Computational Science, ICCS 2013, 2013. ,
DOI : 10.1016/j.procs.2013.05.165
URL : https://hal.archives-ouvertes.fr/hal-00809024
Complex molecular assemblies at hand via interactive simulations, J. Comput. Chem, vol.30, issue.15, pp.2375-2387, 2009. ,
DOI : 10.1002/jcc.21235
URL : https://hal.archives-ouvertes.fr/inserm-00713313
Computer simulation of protein folding, Nature, vol.253, issue.5494, pp.694-698, 1975. ,
Protein-folding dynamics, Nature, vol.260, issue.5550, pp.404-406, 1976. ,
Coarse-grained modelling of DNA and DNA self-assembly ,
Simulating the Physical World: Hierarchical Modeling from Quantum Mechanics to Fluid Dynamics, 2007. ,
The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems, Chemical Society reviews, vol.43, issue.13, pp.4871-4893, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01084631
The Amber biomolecular simulation programs, Journal of Computational Chemistry, vol.26, issue.16, pp.1668-1688, 2005. ,
Fast and Scriptable Molecular Graphics in Web Browsers without Java3d, Nature Precedings, issue.713, 2007. ,
VARNA: Interactive drawing and editing of the RNA secondary structure, Bioinformatics, vol.25, issue.15, pp.1974-1975, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00432548
Solution structure of Cobalt(III)Hexammine complexed to the GAAA tetraloop, and metal-ion binding to G·A mismatches11edited by D. E. Draper, Journal of Molecular Biology, vol.295, issue.5, pp.1211-1223, 2000. ,
Structure of the Intact Stem and Bulge of HIV-1 ?-RNA Stem-Loop SL1, Journal of Molecular Biology, vol.326, issue.2, pp.529-542, 2003. ,
NMR structure of the Aquifex aeolicus tmRNA pseudoknot PK1: new insights into the recoding event of the ribosomal trans-translation, Nucleic Acids Research, vol.34, issue.6, pp.1847-1853, 2006. ,
Solution Structure and Dynamics of the Wild-type Pseudoknot of Human Telomerase RNA, Journal of Molecular Biology, vol.384, issue.5, pp.1249-1261, 2008. ,
Web Protocols and Practice: HTTP/1.1, Networking Protocols, Caching, and Traffic Measurement, 2001. ,
, The Web framework for perfectionists with deadlines | Django
,
, Distributed Task Queue
Biopython: freely available Python tools for computational molecular biology and bioinformatics, Bioinformatics, vol.25, issue.11, pp.1422-1423, 2009. ,
,
, CentOS Project
, uwsgi: uWSGI application server container, vol.25, p.31, 2017.
, Welcome to The Apache Software Foundation!
, RabbitMQ -Messaging that just works
,
Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments. Nucleic Acids Research, vol.38, pp.6313-6323, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00533099
Adaptive resolution simulation of oligonucleotides, The Journal of Chemical Physics, vol.145, issue.23, p.234101, 2016. ,
Amyloid ? Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies, Chemical Reviews, vol.115, issue.9, pp.3518-3563, 2015. ,
Study on A?34 biology and detection in transgenic mice brains, Neurobiology of Aging, vol.35, issue.7, pp.1570-1581, 2014. ,
Slow dynamics in protein fluctuations revealed by time-structure based independent component analysis: The case of domain motions, The Journal of Chemical Physics, vol.134, issue.6, p.65101, 2011. ,
Sampling the complex energy landscape of a simple ?-hairpin, The Journal of Chemical Physics, vol.119, issue.13, pp.6403-6406, 2003. ,
Wide Exploration of OPEP Protein Energy Landscapes using Advanced Monte Carlo Methods, Biophysical Journal, vol.106, issue.2, p.256, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01498048
Kinetics and energetics of base-pair opening in 5'-d(CGCGAATTCGCG)-3' and a substituted dodecamer containing G.T mismatches, Biochemistry, issue.36, pp.8421-8428, 1992. ,
1h NMR determination of base-pair lifetimes in oligonucleotides containing single base mismatches, Nucleic Acids Research, vol.30, issue.21, pp.4740-4750, 2002. ,
, Annalen der Physik, vol.351, issue.6, pp.809-823, 1915.
Virtual Reality Peripheral Network -Official GitHub Repository, 2017. ,
Simulator sickness: a problem for Army aviation, Aviation, Space, and Environmental Medicine, vol.58, issue.4, pp.355-357, 1987. ,
A Discussion of Cybersickness in Virtual Environments, SIGCHI Bull, vol.32, issue.1, pp.47-56, 2000. ,
New VR Navigation Techniques to Reduce Cybersickness. Electronic Imaging, pp.48-53, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01779593
A Modified Version of the Cornell et al. Force Field with Improved Sugar Pucker Phases and Helical Repeat, Journal of Biomolecular Structure and Dynamics, vol.16, issue.4, pp.845-862, 1999. ,
Protein-protein docking with a reduced protein model accounting for side-chain flexibility, Protein Science: A Publication of the Protein Society, vol.12, issue.6, pp.1271-1282, 2003. ,
DOI : 10.1110/ps.0239303
URL : https://onlinelibrary.wiley.com/doi/pdf/10.1110/ps.0239303
Modeling correlated main-chain motions in proteins for flexible molecular recognition, Proteins: Structure, Function, and Bioinformatics, vol.57, issue.2, pp.243-261, 2004. ,
DOI : 10.1002/prot.20179
URL : http://www.cs.duke.edu/~brd/Teaching/Bio/asmb/current/Papers/NMA/zavodsky-proteins-sfb-2004.pdf
IMPALA: A simple restraint field to simulate the biological membrane in molecular structure studies, Proteins: Structure, Function, and Bioinformatics, vol.30, issue.4, pp.357-371, 1998. ,
Visualisation et simulations numériques avancées en biologie : applications au complexe SNARE impliqué dans la fusion membranaire, vol.6, 2012. ,
Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open\textless-\textgreaterclosed transitions, Journal of Molecular Biology, vol.394, issue.1, pp.160-176, 2009. ,
Crystal structure of the guanylate kinase domain from discs large homolog 1 (DLG1/SAP97), Biochemical and Biophysical Research Communications, vol.435, issue.3, pp.334-338, 2013. ,
A new cytokine-receptor binding mode revealed by the crystal structure of the IL-1 receptor with an antagonist, Nature, vol.386, issue.6621, pp.194-200, 1997. ,
, Les origines moléculaires de la vie
, , 2010.
GPU-accelerated atom and dynamic bond visualization using hyperballs: a unified algorithm for balls, sticks, and hyperboloids, J. Comput. Chem, vol.32, issue.13, pp.2924-2935, 2011. ,
DOI : 10.1002/jcc.21861
URL : https://hal.archives-ouvertes.fr/hal-00645162
Predicting protein structures with a multiplayer online game, Nature, vol.466, issue.7307, pp.756-760, 2010. ,
DOI : 10.1038/nature09304
URL : http://europepmc.org/articles/pmc2956414?pdf=render
Coarse-grained simulations of RNA and DNA duplexes, J. Phys. Chem. B, vol.117, issue.27, pp.8047-8060, 2013. ,
DOI : 10.1021/jp400786b
URL : https://hal.archives-ouvertes.fr/hal-01498061
Complex molecular assemblies at hand via interactive simulations, J. Comput. Chem, vol.30, issue.15, pp.2375-2387, 2009. ,
DOI : 10.1002/jcc.21235
URL : https://hal.archives-ouvertes.fr/inserm-00713313
Steered molecular dynamics studies of titin i1 domain unfolding, Biophysical Journal, vol.83, issue.6, pp.3435-3445, 2002. ,
DOI : 10.1016/s0006-3495(02)75343-5
URL : https://doi.org/10.1016/s0006-3495(02)75343-5
Molecular simulations and visualization: introduction and overview, Faraday Discussions, vol.169, issue.0, pp.9-22, 2014. ,
DOI : 10.1039/c4fd90024c
URL : https://hal.archives-ouvertes.fr/hal-01084628
VMD: visual molecular dynamics, Journal of Molecular Graphics, vol.14, issue.1, pp.27-28, 1996. ,
Game on, science -how video game technology may help biologists tackle visualization challenges, PLoS ONE, vol.8, issue.3, p.57990, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-01084644
Innovative interactive flexible docking method for multi-scale reconstruction elucidates dystrophin molecular assembly, Faraday Discuss, vol.169, pp.45-62, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01018071
HiRE-RNA: a high resolution coarsegrained energy model for RNA, J. Phys. Chem. B, vol.114, issue.37, pp.11957-11966, 2010. ,
Three-dimensional representations of complex carbohydrates and polysaccharidesSweetUnityMol: A video game-based computer graphic software. Glycobiology, page cwu133, 2014. ,
Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments, Nucleic Acids Res, vol.38, issue.19, pp.6313-6336, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00533099
Advances in human-protein interaction -interactive and immersive molecular simulations, Protein-Protein Interactions -Computational and Experimental Tools, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00760181
Content-guided navigation in multimeric molecular complexes, BIOIMAGING 2014 -Proceedings of the International Conference on Bioimaging, pp.76-81, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01498053
UNITYMOL: INTERACTIVE AND LUDIC VISUAL MANIPULATION OF COARSE REFERENCES ,
The nucleic acid database, Acta Crystallogr. D Biol. Crystallogr, vol.58, pp.889-898, 2002. ,
The non-WatsonCrick base pairs and their associated isostericity matrices, Nucleic Acids Res, vol.30, pp.3497-3531, 2002. ,
RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction, RNA, vol.18, pp.610-625, 2012. ,
RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures, RNA, vol.21, pp.1066-1084, 2015. ,
RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme, RNA, vol.23, pp.655-672, 2017. ,
Modeling complex RNA tertiary folds with ROSETTA, Methods Enzymol, vol.553, pp.35-64, 2015. ,
The MC-fold and MC-sym pipeline infers RNA structure from sequence data, Nature, vol.452, pp.51-55, 2008. ,
NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure, Nucleic Acids Res, vol.38, pp.280-282, 2010. ,
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information, Nucleic Acids Res, vol.9, pp.133-148, 1981. ,
Fast algorithm for predicting the secondary structure of single-stranded RNA, Proc. Natl. Acad. Sci. USA, vol.77, pp.6309-6313, 1980. ,
An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots, Bioinformatics, vol.20, pp.58-66, 2004. ,
A dynamic programming algorithm for RNA structure prediction including pseudoknots, J. Mol. Biol, vol.285, pp.2053-2068, 1999. ,
RNA pseudoknot prediction in energy-based models, J. Comput. Biol, vol.7, pp.409-427, 2000. ,
RNA 3D structure prediction by using a coarse-grained model and experimental data, J. Phys. Chem. B, vol.117, pp.3135-3144, 2013. ,
Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms, RNA, vol.14, pp.1164-1173, 2008. ,
A nucleotide-level coarsegrained model of RNA, Interactive RNA Folding Simulations Biophysical Journal, vol.113, p.235102, 2014. ,
HiRE-RNA: a high resolution coarse-grained energy model for RNA, J. Phys. Chem. B, vol.114, pp.11957-11966, 2010. ,
Ab initio RNA folding, J. Phys. Condens. Matter, vol.27, p.233102, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01498011
, Coarse-grained simu, 2016.
, J. Chem. Theory Comput, vol.12, pp.6077-6097
Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures, Proc. Natl. Acad. Sci. USA, vol.106, pp.17349-17354, 2009. ,
Modelling toeholdmediated RNA strand displacement, Biophys. J, vol.108, pp.1238-1247, 2015. ,
Molecular mechanism of the inhibition of EGCG on the Alzheimer Ab(1-42) dimer, J. Phys. Chem. B, vol.117, pp.3993-4002, 2013. ,
Predicting protein structures with a multiplayer online game, Nature, vol.466, pp.756-760, 2010. ,
RNA design rules from a massive open laboratory, Proc. Natl. Acad. Sci. USA, vol.111, pp.2122-2127, 2014. ,
Coarse-grained HiRE-RNA model for ab initio RNA folding beyond simple molecules, including noncanonical and multiple base pairings, J. Chem. Theory Comput, vol.11, pp.3510-3522, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01498008
Game on, science-how video game technology may help biologists tackle visualization challenges, PLoS One, vol.8, p.57990, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-01084644
Unitymol: interactive and ludic visual manipulation of coarse-grained RNA and other biomolecules, 2015 IEEE 1st International Workshop on Virtual and Augmented Reality for Molecular Science, pp.1-6, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01498023
The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems, Chem. Soc. Rev, vol.43, pp.4871-4893, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01084631
The coarse-grained OPEP force field for non-amyloid and amyloid proteins, J. Phys. Chem. B, vol.116, pp.8741-8752, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-01498091
Communication: simulated tempering with fast on-the-fly weight determination, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-01498062
, J. Chem. Phys, vol.138, p.61102
Three-dimensional representations of complex carbohydrates and polysaccharides-sweetunityMol: a video game-based computer graphic software, Glycobiology, vol.25, pp.483-491, 2015. ,
Solution structure of Cobalt(III) hexammine complexed to the GAAA tetraloop, and metal-ion binding to G.A mismatches, J. Mol. Biol, vol.295, pp.1211-1223, 2000. ,
Structure of the intact stem and bulge of HIV-1 Psi-RNA stem-loop SL1, J. Mol. Biol, vol.326, pp.529-542, 2003. ,
NMR structure of the Aquifex aeolicus tmRNA pseudoknot PK1: new insights into the recoding event of the ribosomal trans-translation, Nucleic Acids Res, vol.34, pp.1847-1853, 2006. ,
Solution structure and dynamics of the wild-type pseudoknot of human telomerase RNA, J. Mol. Biol, vol.384, pp.1249-1261, 2008. ,
Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design, Nucleic Acids Res, vol.31, pp.2926-2943, 2003. ,
RAG: RNA-As-Graphs web resource, BMC Bioinformatics, vol.5, p.88, 2004. ,
Vfold: a web server for RNA structure and folding thermodynamics prediction, PLoS One, vol.9, p.107504, 2014. ,
Algorithm discovery by protein folding game players, Proc. Natl. Acad. Sci. USA, vol.108, pp.18949-18953, 2011. ,
Complex molecular assemblies at hand via interactive simulations, J. Comput. Chem, vol.30, pp.2375-2387, 2009. ,
URL : https://hal.archives-ouvertes.fr/inserm-00713313
,
, Biophysical Journal, vol.113, pp.302-312, 2017.
Secondary structure of single-stranded nucleic acids, Advances in mathematics supplementary studies, vol.1, pp.167-212, 1978. ,
Exploring the repertoire of rna secondary motifs using graph theory; implications for rna design, Nucleic Acids Res, vol.31, pp.2926-2943, 2003. ,
Rag: Rna-as-graphs web resource, BMC Bioinf, vol.5, p.88, 2004. ,
A System for Interactive Molecular Dynamics Simulation, Proceedings of the 2001 Symposium on Interactive 3D Graphics. I3D '01, pp.191-194, 2001. ,
Complex molecular assemblies at hand via interactive simulations, J Comput Chem, vol.30, pp.2375-2387, 2009. ,
URL : https://hal.archives-ouvertes.fr/inserm-00713313
Interactive Molecular Dynamics: Scaling up to Large Systems, International Conference on Computational Science, ICCS 2013, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-01084652
Will chemists tilt their heads for virtual reality?, vol.94, 2016. ,
Coarse-grained simulations of rna and dna duplexes, J Phys Chem B, vol.117, pp.8047-8060, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-01498061
, Acc. Chem. Res, vol.48, p.3026, 2015.
, Curr. Opin. Struct. Biol, vol.25, p.67, 2014.
, Angew. Chem. Int. Ed. Engl, vol.53, p.9992, 2014.
, Cell, vol.155, p.1199, 2013.
, Nature, vol.253, p.694, 1975.
, Annu. Rev. Biophys, vol.42, p.73, 2013.
, Chem. Soc. Rev, vol.42, p.6801, 2013.
, J. Am. Chem. Soc, vol.128, p.2697, 2006.
, PLoS Comput. Biol, vol.9, p.1003034, 2013.
, J. Phys. Chem. B, vol.110, p.3674, 2006.
, J. Chem. Theory Comput, vol.5, p.2115, 2009.
, Methods Enzymol, vol.523, p.109, 2013.
, Proteins, vol.78, p.2950, 2010.
, J. Chem. Theory Comput, vol.9, p.785, 2013.
, Proteins, vol.81, p.81, 2013.
, J. Phys. Chem. B, vol.116, p.8494, 2012.
, J. Chem. Theory Comput, vol.9, p.803, 2013.
, J. Chem. Phys, vol.130, p.235106, 2009.
, ACS Nano, vol.11, p.1000, 2017.
, J. Chem. Phys, vol.145, p.224107, 2016.
, J. Chem. Phys, vol.145, p.234101, 2016.
, Proc. Natl. Acad. Sci. U. S. A, vol.114, p.3370, 2017.
, Curr. Opin. Struct. Biol, vol.42, p.24, 2017.
, J. Chem. Theory Comput, vol.12, p.6077, 2016.
, Curr. Opin. Struct. Biol, vol.40, p.8, 2016.
, Chem. Rev, vol.116, p.7898, 2016.
, Chem. Soc. Rev, vol.43, p.4871, 2014.
, J. Chem. Theory Comput, vol.11, p.1843, 2015.
, Philos. Trans. A, vol.374, p.20160225, 2016.
, J. Chem. Phys, vol.106, p.5260, 1997.
, J. Chem. Phys, vol.111, p.2301, 1999.
, J. Phys. Chem. B, vol.116, p.8741, 2012.
, J. Chem. Theory. Comput, vol.9, p.4574, 2013.
, Phys. Rev. Lett, vol.85, p.206, 2000.
, Proteins, vol.45, p.159, 2001.
, J. Chem. Phys, vol.119, p.6403, 2003.
, J. Chem. Phys, vol.117, p.11379, 2002.
, Proteins, vol.65, p.180, 2006.
, J. Chem. Phys, vol.122, p.174904, 2005.
, J. Chem. Phys, vol.126, p.25101, 2007.
, J. Chem. Theory Comput, vol.7, p.1502, 2011.
, PLoS Comput. Biol, vol.7, p.1002051, 2011.
, J. Chem. Theory Comput, vol.14, p.1928, 2011.
, J. Chem. Phys, vol.138, p.61102, 2013.
, J. Phys. Chem. B, vol.119, p.6941, 2015.
, J. Chem. Theory Comput, vol.10, p.4745, 2014.
, Nucleic Acids Res, vol.40, p.288, 2012.
, J. Non Cryst. Solids, vol.407, p.494, 2015.
, , vol.9, p.4, 2016.
, J. Phys. Chem. B, vol.114, p.11957, 2010.
, J. Phys. Chem. B, vol.117, p.8047, 2013.
, Biophys. J, vol.87, p.3648, 2004.
, J. Phys. Chem. B, vol.112, p.4410, 2008.
, Science, vol.335, p.1228, 2012.
, J. Chem. Phys, vol.132, p.165103, 2010.
, J. Chem. Phys, vol.145, p.35102, 2016.
, Handbook of Molecular Biology, pp.1-24, 2006.
, Biochemistry, vol.24, p.1501, 1985.
, Biochemistry, vol.49, p.11, 1994.
, J. Mol. Biol, vol.357, p.1335, 2006.
, Macromolecules, vol.18, p.534, 1985.
, Chem. Rev, vol.116, p.7898, 2016.
, Science, vol.250, p.1121, 1990.
, Proc. Natl. Acad. Sci. U. S. A, vol.96, p.1273, 1996.
, Nature, vol.369, p.248, 1994.
, Proc. Natl. Acad. Sci. U. S. A, vol.90, p.6369, 1993.
, J. Chem. Phys, vol.110, p.1252, 1999.
, Annu. Rev. Phys. Chem, vol.62, p.301, 2011.
, J. Chem. Phys, vol.129, p.175101, 2008.
, Phys. Rev. Lett, vol.105, p.218101, 2010.
, Phys. Rev. Lett, vol.110, p.58101, 2013.
, PLoS Comput. Biol, vol.4, p.1000241, 2008.
, Biophy. J, vol.100, p.693, 2011.
, PLoS One, vol.9, p.85185, 2014.
, PLoS Comput. Biol, vol.11, p.1004277, 2015.
, Phys. Rev. Lett, vol.111, p.58101, 2003.
, J. Chem. Phys, vol.107, p.1941, 1997.
, J. Chem. Phys, vol.144, p.205103, 2016.
, Phys. Chem. Chem. Phys, vol.13, p.9778, 2011.
, Nature, vol.447, issue.7143, pp.453-457, 2007.
, Curr. Opin. Struct. Biol, vol.16, p.260, 2006.
, Isr. J. Chem, vol.57, p.564, 2017.
, Ann. Rev. Biophys, vol.37, p.399, 2008.
, Blood, vol.124, p.1412, 2014.
, Proc. Natl. Acad. Sci. U. S. A, vol.112, p.9884, 2015.
, Nat. Comm, vol.7, p.10738, 2015.
, Sci. Adv, vol.3, p.1601944, 2017.
, J. Chem. Theory. Comput, vol.9, p.4574, 2013.
, Biophys. J, vol.98, p.35, 2010.
, J. Chem. Phys, vol.127, p.155106, 2007.
, Biophys. J, vol.113, p.302, 2017.
, Chem. Rev, p.115
, / Biochemical and Biophysical Research Communications, pp.1-9, 2017.
Multi-scale simulations of biological systems using the OPEP coarse-grained model, Biochemical and Biophysical Research Communications, p.3518, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01644564
, Neurobiol. Aging, vol.35, p.1570, 2014.
, Proceedings of the 2001 Symposium on Interactive 3D Graphics, 2001.
, J. Comput. Chem, vol.30, p.2375, 2009.
, Procedia Comput. Sci, vol.18, p.20, 2013.
, PLoS One, vol.8, p.57990, 2013.
, Biophys. J, vol.106, p.256, 2014.
, Acc. Chem. Res, vol.47, p.603, 2014.
, Curr. Opin. Struct. Biol, vol.30, p.50, 2015.
, ACS Chem. Neurosci, vol.8, p.1435, 2017.
, Biochemical and Biophysical Research Communications, pp.1-9, 2017.
, UnityMol: Interactive and Ludic Visual Manipulation of Coarse-Grained RNA and other Biomolecules Sébastien Doutreligne, Marc Baaden Biophysical Journal, 2017.
Multi-scale and Multi-physics Simulations of Biological Systems using the OPEP Coarse-grained Model Fabio Sterpone, Simone Melchionna, Marc Baaden, Phuong H. Nguyen, and Philippe Derreumaux -BioSpring: multi-scale modeling with spring networks Sébastien Doutreligne, 2017. ,
, UnityMol: Interactive Scientific Visualization for Integrative Biology Sébastien Doutreligne, vol.9080
Game on, science -how video game technology may help biologists tackle visualization challenges, PLoS ONE, vol.8, issue.3, p.57990, 2013. ,
DOI : 10.1371/journal.pone.0057990
URL : https://hal.archives-ouvertes.fr/hal-01084644
GPU-accelerated atom and dynamic bond visualization using hyperballs: a unified algorithm for balls, sticks,and hyperboloids, J. Comput. Chem, vol.32, issue.13, pp.2924-2935, 2011. ,
DOI : 10.1002/jcc.21861
URL : https://hal.archives-ouvertes.fr/hal-00645162
Complex molecular assemblies at hand via interactive simulations, J. Comput. Chem, vol.30, issue.15, pp.2375-2387, 2009. ,
DOI : 10.1002/jcc.21235
URL : https://hal.archives-ouvertes.fr/inserm-00713313
HiRE-RNA: a high resolution coarse-grained energy model for RNA, J. Phys. Chem. B, vol.114, issue.37, pp.11957-11966, 2010. ,
VARNA: Interactive drawing and editing of the RNA secondary structure, Bioinformatics, vol.25, issue.15, pp.1974-1975, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00432548
HiRE-RNA: a high resolution coarse-grained energy model for RNA, J. Phys. Chem. B, vol.114, issue.37, pp.11957-11966, 2010. ,
DOI : 10.1021/jp102497y
Coarse-grained simulations of RNA and DNA duplexes, J. Phys. Chem. B, vol.117, issue.27, pp.8047-8060, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-01498061
Game on, science -how video game technology may help biologists tackle visualization challenges, PLoS ONE, vol.8, issue.3, p.57990, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-01084644
Three-dimensional representations of complex carbohydrates and polysaccharides -Sweet UnityMol: A video game-based computer graphic software, Glycobiology, p.133, 2014. ,
, UnityMol pour l'éducation des études structurales des molécules d'ADN, ARN et protéines. Une des applications possibles est l'enseignement. Entre mai 2015 et aujourd'hui, nous
, Ce travail a be?ne?ficiebe?ne?be?ne?ficie d'une aide de l'Etat ge?reége?reé par l'Agence Nationale de la Recherche au titre du programme Investissements
A modified version of the cornell et al. force field with improved sugar pucker phases and helical repeat, Journal of Biomolecular Structure and Dynamics, vol.16, issue.4, p.10217454, 1999. ,
Protein-protein docking with a reduced protein model accounting for sidechain flexibility, Protein Science: A Publication of the Protein Society, vol.12, issue.6, pp.1271-1282, 2003. ,
Electrostatics of nanosystems: Application to microtubules and the ribosome, Proc. Natl. Acad. Sci. USA, vol.98, pp.10-037, 2001. ,
Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics, Structure, vol.16, issue.5, pp.673-683, 1993. ,
IMPALA: A simple restraint field to simulate the biological membrane in molecular structure studies, Proteins: Structure, Function, and Bioinformatics, vol.30, issue.4, pp.357-371, 1998. ,
Multihaptic device, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, pp.205-215, 2010. ,
Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments, Nucleic Acids Research, vol.38, issue.19, pp.6313-6323, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00533099
Innovative interactive flexible docking method for multi-scale reconstruction elucidates dystrophin molecular assembly, Faraday Discuss, vol.169, issue.0, pp.45-62, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01018071
Structural Basis of Neuronal Nitric-Oxide Synthase Interaction with Dystrophin Repeats 16 and 17, Journal of Biological Chemistry, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01214011
VMD -Visual Molecular Dynamics, J. Molec. Graphics, vol.14, pp.33-38, 1996. ,
Game on, Science -how video game technology may help biologists tackle visualization challenges, PLoS ONE, vol.8, issue.3, p.57990 ,
URL : https://hal.archives-ouvertes.fr/hal-01084644
Analysis of domain motions by approximate normal mode calculations, Proteins: Structure, Function, and Bioinformatics, vol.33, issue.3, pp.417-429, 1998. ,
URL : https://hal.archives-ouvertes.fr/hal-02159766