Motion planning algorithms for molecular simulations: A survey, Computer Science Review, vol.6, issue.4, pp.125-168, 2012. ,
DOI : 10.1016/j.cosrev.2012.07.002
URL : https://hal.archives-ouvertes.fr/hal-01982596
Asymptotically Optimal Design of Piecewise Cylindrical Robots using Motion Planning, Robotics: Science and Systems XIII, 2017. ,
DOI : 10.15607/RSS.2017.XIII.020
Optimizing design parameters for sets of concentric tube robots using sampling-based motion planning, 2015 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS), pp.4381-4387, 2015. ,
DOI : 10.1109/IROS.2015.7353999
Coarse-grained sequences for protein folding and design, Proceedings of the National Academy of Sciences, vol.8, issue.1, pp.10712-10717, 2003. ,
DOI : 10.1016/S0969-2126(00)00130-1
Sampling-Based Motion Planning under Kinematic Loop-Closure Constraints, Algorithmic Foundations of Robotics VI, pp.75-90, 2005. ,
DOI : 10.1007/10991541_7
Geometric algorithms for the conformational analysis of long protein loops, Journal of Computational Chemistry, vol.9, issue.Suppl, pp.956-967, 2004. ,
DOI : 10.1109/ROBOT.2001.932673
A multitree extension of the transition-based RRT: Application to ordering-and-pathfinding problems in continuous cost spaces, Proc. IEEE/RSJ International Conference on Intelligent Robots and Systems, pp.2991-2996, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01057030
Optimal Path Planning in Complex Cost Spaces With Sampling-Based Algorithms, IEEE Transactions on Automation Science and Engineering, vol.13, issue.2, pp.415-424, 2016. ,
DOI : 10.1109/TASE.2015.2487881
URL : https://hal.archives-ouvertes.fr/hal-01231482
, Algorithms in Structural Molecular Biology, 2011.
Hybrid parallelization of a multi-tree path search algorithm: Application to highly-flexible biomolecules, Parallel Computing, vol.77 ,
DOI : 10.1016/j.parco.2018.06.005
Dynamics of a flexible loop in dihydrofolate reductase from Escherichia coli and its implication for catalysis, Biochemistry, vol.33, issue.2, pp.439-442, 1994. ,
DOI : 10.1021/bi00168a007
Computational Models of Protein Kinematics and Dynamics: Beyond Simulation, Annual Review of Analytical Chemistry, vol.5, issue.1, pp.273-91, 2012. ,
DOI : 10.1146/annurev-anchem-062011-143024
A Global Performance Index for the Kinematic Optimization of Robotic Manipulators, Journal of Mechanical Design, vol.113, issue.3, pp.220-226, 1991. ,
DOI : 10.1115/1.2912772
The minimum constraint removal problem with three robotics applications, The International Journal of Robotics Research, vol.33, issue.1, pp.5-17, 2014. ,
DOI : 10.1007/978-3-540-68405-3_17
URL : http://www.cs.indiana.edu/%7Ehauserk/papers/wafr2012-constraintremoval.pdf
Multi-modal Motion Planning in Non-expansive Spaces, The International Journal of Robotics Research, vol.27, issue.11, pp.897-915, 2010. ,
DOI : 10.1002/rob.20193
URL : http://www.stanford.edu/~khauser/papers/wafr08-multimodal.pdf
Sampling-Based Path Planning on Configuration-Space Costmaps, IEEE Transactions on Robotics, vol.26, issue.4, pp.635-646, 2010. ,
DOI : 10.1109/TRO.2010.2049527
URL : http://upcommons.upc.edu/bitstream/2117/12361/1/jaillet.pdf
Fast marching tree: A fast marching sampling-based method for optimal motion planning in many dimensions, The International Journal of Robotics Research, vol.35, issue.3, pp.883-921, 2015. ,
DOI : 10.1109/MRA.2013.2248309
URL : http://europepmc.org/articles/pmc4798023?pdf=render
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features, Biopolymers, vol.33, issue.12, pp.2577-2637, 1983. ,
DOI : 10.1016/0005-2795(73)90350-4
Sampling-based algorithms for optimal motion planning, The International Journal of Robotics Research, vol.9, issue.7, pp.846-894, 2011. ,
DOI : 10.1109/TRO.2006.886840
URL : http://arxiv.org/pdf/1105.1186
Probabilistic roadmaps for path planning in high-dimensional configuration spaces, IEEE Transactions on Robotics and Automation, vol.12, issue.4, pp.566-580, 1996. ,
DOI : 10.1109/70.508439
URL : http://archive.cs.uu.nl/pub/RUU/CS/techreps/CS-1994/1994-32.ps.gz
Methods in protein design, Methods in enzymology, vol.523, 2013. ,
Planning Algorithms, 2006. ,
DOI : 10.1017/CBO9780511546877
Rapidly-exploring random trees : Progress and prospects, Algorithmic and Computational Robotics, pp.293-308, 2001. ,
Functional role of a mobile loop of Escherichia coli dihydrofolate reductase in transition-state stabilization, Biochemistry, vol.31, issue.34, pp.7826-7833, 1992. ,
DOI : 10.1021/bi00149a012
Asymptotically optimal sampling-based kinodynamic planning, The International Journal of Robotics Research, vol.230, issue.5, pp.528-564, 2016. ,
DOI : 10.1177/0278364913488805
URL : http://arxiv.org/pdf/1407.2896
Kinematic synthesis Formal Engineering Design Synthesis, 2001. ,
Optimal design of robots, Robotics: Science and Systems I, pp.8-11, 2005. ,
DOI : 10.15607/RSS.2005.I.041
URL : https://hal.archives-ouvertes.fr/inria-00000473
Equation of State Calculations by Fast Computing Machines, The Journal of Chemical Physics, vol.21, issue.6, pp.1087-1092, 1953. ,
DOI : 10.1063/1.1700747
URL : https://www.osti.gov/servlets/purl/4390578
Roadmap Methods for Protein Folding, 2007. ,
DOI : 10.1385/1-59745-574-1:219
URL : http://www.cs.rice.edu/~mmoll/publications/moll2007roadmap-methods-for-protein-folding.pdf
, Biochemistry, vol.40, issue.33, pp.9846-9859, 2001.
DOI : 10.1021/bi010621k
Iterative approach to computational enzyme design, Proceedings of the National Academy of Sciences, pp.3790-3795, 2012. ,
DOI : 10.1006/jmbi.2000.3758
Multiobjective design and path planning optimization of unmanned aerial vehicles, Proc. 16th AIAA/ISSMO Multidisciplinary Analysis and Optimization Conference, 2015. ,
Probabilistic search and optimization for protein energy landscapes, Handbook of Computational Molecular Biology, 2013. ,
Manipulation Planning with Probabilistic Roadmaps, The International Journal of Robotics Research, vol.23, issue.7-8, pp.729-746, 2004. ,
DOI : 10.1163/156855300741960
Computational design of ligand-binding proteins with high affinity and selectivity, Nature, vol.27, issue.7466, pp.212-218, 2013. ,
DOI : 10.1093/bioinformatics/btr577
A series of PDB-related databanks for everyday needs, Nucleic Acids Research, vol.38, issue.D1, pp.364-368, 2015. ,
DOI : 10.1093/nar/gkq453
Geometric Optimization of Serial Chain Manipulator Structures for Working Volume and Dexterity, The International Journal of Robotics Research, vol.14, issue.4, pp.91-103, 1986. ,
DOI : 10.1115/1.3267349