French summary sophistiquées, par exemple des méthodes faisant intervenir de l'apprentissage, afin de limiter la recherche à un nombre restreint de design et de contrôler la taille de l'arbre d'exploration. Bibliography [Al-Bluwi 2012] Ibrahim Al-Bluwi, Thierry Siméon and Juan Cortés. Motion planning algorithms for molecular simulations: A survey, Computer Science Review, vol.6, issue.94, pp.125-143 ,
Dramatic performance enhancements for the FASTER optimization algorithm, Journal of Computational Chemistry, vol.27, issue.97, pp.1071-1075, 2006. ,
Computational protein design as a cost function network optimization problem, Principles and Practice of Constraint Programming, pp.840-849 ,
Computational protein design as an optimization problem, Artificial Intelligence, vol.212, issue.97, pp.59-79, 2014. ,
DOI : 10.1016/j.artint.2014.03.005
Dihedral angle principal component analysis of molecular dynamics simulations, The Journal of Chemical Physics, vol.62, issue.24, p.244111, 2007. ,
DOI : 10.1063/1.475378
OBPRM: An Obstacle-based PRM for 3D Workspaces The Algorithmic Perspective: The Algorithmic Perspective, Proceedings of the Third Workshop on the Algorithmic Foundations of Robotics on Robotics WAFR '98, pp.155-168, 1998. ,
Using Motion Planning to Map Protein Folding Landscapes and Analyze Folding Kinetics of Known Native Structures, Journal of Computational Biology, vol.10, issue.3-4, pp.239-255, 2003. ,
DOI : 10.1089/10665270360688002
The formation and stabilization of protein structure, Biochemical Journal, vol.128, issue.4, pp.737-749, 1972. ,
DOI : 10.1042/bj1280737
Finite-time analysis of the multiarmed bandit problem, Machine Learning, vol.47, issue.2/3, pp.235-256, 2002. ,
DOI : 10.1023/A:1013689704352
Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation 1 1 Edited by B. Honig, Journal of Molecular Biology, vol.266, issue.1, pp.195-214, 1997. ,
DOI : 10.1006/jmbi.1996.0758
Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations, Journal of Structural Biology, vol.157, issue.3, pp.514-523, 2007. ,
The Protein Data Bank, Nucleic Acids Research, vol.28, issue.1, pp.235-242, 2000. ,
DOI : 10.1093/nar/28.1.235
A structural model for unfolded proteins from residual dipolar couplings and small-angle x-ray scattering, Proceedings of the National Academy of Sciences, vol.102, issue.37, pp.17002-17007, 2005. ,
DOI : 10.1073/pnas.0506078102
URL : http://www.pnas.org/content/102/47/17002.full.pdf
Efficient Monte Carlo trial moves for polypeptide simulations, The Journal of Chemical Physics, vol.123, issue.17, pp.174905-174905, 2005. ,
DOI : 10.1073/pnas.96.20.11311
-Designed Peptides:?? Design and Characterization of Antiparallel Four-Stranded Coiled Coils, Biochemistry, vol.35, issue.21, pp.6955-6962, 1996. ,
DOI : 10.1021/bi960095a
URL : https://hal.archives-ouvertes.fr/pasteur-00166857
Simulated tempering yields insight into the low-resolution Rosetta scoring functions, Proteins, vol.74, issue.3, pp.777-788, 2009. ,
CHARMM: The biomolecular simulation program, Journal of Computational Chemistry, vol.103, issue.13, pp.1545-1614, 2009. ,
DOI : 10.1021/ci034261e
Coarsegrained sequences for protein folding and design, Proceedings of the National Academy of Sciences, pp.10712-10717, 2003. ,
Real-time randomized path planning for robot navigation, IEEE/RSJ International Conference on Intelligent Robots and Systems, pp.2383-2388, 2002. ,
Guiding conformation space search with an all-atom energy potential, Proteins: Structure, Function, and Bioinformatics, vol.22, issue.Suppl. 6, pp.958-972, 2008. ,
DOI : 10.1002/prot.10556
Cyclic coordinate descent: A robotics algorithm for protein loop closure, Protein Science, vol.12, issue.5, pp.963-972, 2003. ,
Finding pathways between distant local minima, The Journal of Chemical Physics, vol.122, issue.23, p.234903, 2005. ,
The challenge of considering receptor flexibility in ligand docking and virtual screening, Current Computer-Aided Drug Design, vol.1, issue.4, pp.423-440, 2005. ,
Resolution complete rapidly-exploring random trees, Proceedings 2002 IEEE International Conference on Robotics and Automation (Cat. No.02CH37292), pp.267-272, 2002. ,
DOI : 10.1109/ROBOT.2002.1013372
Principles of Robot Motion: Theory, Algorithms, and Implementations, p.17, 2005. ,
Affinity enhancement of an in vivo matured therapeutic antibody using structure-based computational design, Protein Science, vol.51, issue.5, pp.949-960, 2006. ,
DOI : 10.1110/ps.052030506
Coarse-grained models of protein folding: toy models or predictive tools?, Current Opinion in Structural Biology, vol.18, issue.1, pp.10-15, 2008. ,
DOI : 10.1016/j.sbi.2007.10.005
Geometric algorithms for the conformational analysis of long protein loops, Journal of Computational Chemistry, vol.9, issue.Suppl, pp.956-967, 2004. ,
DOI : 10.1089/10665270252935395
A path planning approach for computing large-amplitude motions of flexible molecules, Bioinformatics, vol.21, issue.Suppl 1, pp.116-125, 2005. ,
DOI : 10.1093/bioinformatics/bti1017
Disassembly Path Planning for Complex Articulated Objects, IEEE Transactions on Robotics, vol.24, issue.2, pp.475-481, 2008. ,
DOI : 10.1109/TRO.2008.915464
Relaxation of amorphous multichain polymer systems using inverse kinematics, Polymer, vol.51, issue.17, pp.4008-4014, 2010. ,
DOI : 10.1016/j.polymer.2010.06.019
A Robotics Approach to Enhance Conformational Sampling of Proteins, Volume 4: 36th Mechanisms and Robotics Conference, Parts A and B, pp.1177-1186, 2012. ,
DOI : 10.1115/DETC2012-70105
A kinematic view of loop closure, Journal of Computational Chemistry, vol.25, issue.4, pp.510-528, 2004. ,
Introduction to Robotics: Mechanics and Control. Pearson, Upper Saddle River, N.J, 3 edition édition, 2004. ,
Qiang Cui and Ivet Bahar, editeurs. Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems, 2005. ,
Protein design automation, Protein Science, vol.1, issue.5, pp.895-903, 1996. ,
DOI : 10.1021/ci00020a020
URL : http://onlinelibrary.wiley.com/doi/10.1002/pro.5560050511/pdf
De Novo Protein Design: Fully Automated Sequence Selection, Science, vol.278, issue.5335, pp.82-87, 1997. ,
DOI : 10.1126/science.278.5335.82
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.72.7304
Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction, Proceedings of the National Academy of Sciences, pp.9885-9890, 2006. ,
DOI : 10.1006/jmbi.2000.3693
Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home, Proteins: Structure, Function, and Bioinformatics, vol.100, issue.200, pp.118-128, 2007. ,
DOI : 10.1002/prot.21636
Combining System Design and Path Planning, Workshop on the Algorithmic Foundations of Robotics (WAFR), 2016. ,
Segmenting proteins into tripeptides to enhance conformational sampling with Monte Carlo methods, Journal of Chemical Theory and Computation, p.2017, 2017. ,
Metal-Mediated Affinity and Orientation Specificity in a Computationally Designed Protein Homodimer, Journal of the American Chemical Society, vol.134, issue.1, pp.375-385, 2012. ,
De novo design of the hydrophobic cores of proteins, Protein Science, vol.88, issue.12, pp.2006-2018, 1995. ,
DOI : 10.1080/07391102.1991.10507882
Fast and accurate side-chain topology and energy refinement (FASTER) as a new method for protein structure optimization, Proteins, vol.48, issue.97, pp.31-43, 2002. ,
MoMA-LigPath: a web server to simulate protein-ligand unbinding, Nucleic Acids Research, vol.41, issue.W1, pp.297-302, 2013. ,
DOI : 10.1093/nar/gkt380
A multi-tree approach to compute transition paths on energy landscapes, Workshop on Artificial Intelligence and Robotics Methods in Computational Biology, AAAI'13, pp.8-2013, 2013. ,
A multi-tree extension of the transition-based RRT: Application to ordering-and-pathfinding problems in continuous cost spaces, 2014 IEEE/RSJ International Conference on Intelligent Robots and Systems, pp.2991-2996, 2014. ,
DOI : 10.1109/IROS.2014.6942975
URL : https://hal.archives-ouvertes.fr/hal-01057030
Characterizing Energy Landscapes of Peptides Using a Combination of Stochastic Algorithms, IEEE Transactions on NanoBioscience, vol.14, issue.5, pp.545-552, 2015. ,
DOI : 10.1109/TNB.2015.2424597
URL : https://hal.archives-ouvertes.fr/hal-01143833
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
A note on two problems in connexion with graphs, Numerische Mathematik, vol.4, issue.1, pp.269-271, 1959. ,
DOI : 10.1007/BF01386390
A concerted rotation algorithm for atomistic Monte Carlo simulation of polymer melts and glasses, Molecular Physics, vol.28, issue.4, pp.961-996, 1993. ,
DOI : 10.1021/ma00191a079
On Lattice Protein Structure Prediction Revisited, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.8, issue.6, pp.1620-1632, 2011. ,
DOI : 10.1109/TCBB.2011.41
Parallel Tempering: Theory, Applications, and New Perspectives, Physical Chemistry Chemical Physics, vol.7, issue.94, pp.3910-3927, 2005. ,
Accurate bond and angle parameters for X-ray protein structure refinement, Acta Crystallographica Section A Foundations of Crystallography, vol.47, issue.4, pp.392-400, 1991. ,
DOI : 10.1107/S0108767391001071
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 design of proteins targeting the conserved stem region of influenza hemagglutinin, Science, vol.332, issue.6031, pp.816-821, 2011. ,
A survey of dimension reduction techniques, 2002. ,
Novel formulations for the sequence selection problem in de novo protein design with flexible templates, Optimisation Methods and Software, vol.22, issue.1, pp.51-71, 2007. ,
Toward Full-Sequence De Novo Protein Design with Flexible Templates for Human Beta-Defensin-2, Biophysical Journal, vol.94, issue.96, pp.584-599, 2008. ,
Pairwise decomposition of an MMGBSA energy function for computational protein design, Journal of Computational Chemistry, vol.77, issue.18, pp.1371-1387, 2014. ,
DOI : 10.1002/prot.22488
URL : https://hal.archives-ouvertes.fr/hal-01048588
Protein Design Using Continuous Rotamers, PLoS Computational Biology, vol.285, issue.1, p.1002335, 2012. ,
DOI : 10.1371/journal.pcbi.1002335.s002
URL : http://doi.org/10.1371/journal.pcbi.1002335
Improved Pruning algorithms and Divide-and-Conquer strategies for Dead-End Elimination, with application to protein design, Bioinformatics, vol.22, issue.14, pp.174-183, 2006. ,
DOI : 10.1093/bioinformatics/btl220
URL : https://academic.oup.com/bioinformatics/article-pdf/22/14/e174/615095/btl220.pdf
Dead-End Elimination with Backbone Flexibility, Bioinformatics, vol.23, issue.13, pp.185-194, 2007. ,
DOI : 10.1093/bioinformatics/btm197
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.106.3753
The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles, Journal of Computational Chemistry, vol.23, issue.10, pp.1527-1542, 2008. ,
DOI : 10.1287/ijoc.1040.0096
A Comparative Study of Probabilistic Roadmap Planners, Algorithmic Foundations of Robotics V, numéro 7 de Springer Tracts in Advanced Robotics, pp.43-57, 2004. ,
DOI : 10.1007/978-3-540-45058-0_4
Markov chain Monte Carlo maximum likelihood. Rapport technique, 1991. ,
Ring Closure and Local Conformational Deformations of Chain Molecules, Macromolecules, vol.3, issue.2, pp.178-187, 1970. ,
Efficient rotamer elimination applied to protein side-chains and related spin glasses, Biophysical Journal, vol.66, issue.5, pp.1335-1340, 1994. ,
DOI : 10.1016/S0006-3495(94)80923-3
URL : http://doi.org/10.1016/s0006-3495(94)80923-3
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
Exploring the Folding Free Energy Landscape of a ??-Hairpin Miniprotein, Chignolin, Using Multiscale Free Energy Landscape Calculation Method, The Journal of Physical Chemistry B, vol.115, issue.27, pp.8806-8812, 2011. ,
DOI : 10.1021/jp2008623
Repacking protein cores with backbone freedom: structure prediction for coiled coils., Proceedings of the National Academy of Sciences, vol.92, issue.18, pp.8408-8412, 1995. ,
DOI : 10.1073/pnas.92.18.8408
URL : http://www.pnas.org/content/92/18/8408.full.pdf
A Formal Basis for the Heuristic Determination of Minimum Cost Paths, IEEE Transactions on Systems Science and Cybernetics, vol.4, issue.2, pp.100-107, 1968. ,
DOI : 10.1109/TSSC.1968.300136
Multi-modal Motion Planning in Non-expansive Spaces, The International Journal of Robotics Research, vol.24, issue.5, pp.897-915, 2010. ,
DOI : 10.1002/rob.20193
URL : http://ai.stanford.edu/~latombe/papers/ijrr-09/final.pdf
Exploring conformational space with a simple lattice model for protein structure, Journal of Molecular Biology, vol.243, issue.4, pp.668-682, 1994. ,
Path planning in expansive configuration spaces, IEEE International Conference on Robotics and Automation Proceedings, vol.33, pp.2719-2726, 1997. ,
Randomized single-query motion planning in expansive spaces, 2000. ,
Randomized Kinodynamic Motion Planning with Moving Obstacles, The International Journal of Robotics Research, vol.229, issue.6, pp.233-255, 2002. ,
DOI : 10.1109/70.105387
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.118.9585
High-resolution design of a protein loop, Proceedings of the National Academy of Sciences, vol.26, issue.Pt 3, pp.17668-17673, 2007. ,
DOI : 10.1107/S0021889892009944
Design and structural analysis of alternative hydrophobic core packing arrangements in bacteriophage T4 lysozyme, Journal of Molecular Biology, vol.224, issue.4, pp.1143-1159, 1992. ,
DOI : 10.1016/0022-2836(92)90475-Y
Transition-based RRT for path planning in continuous cost spaces, 2008 IEEE/RSJ International Conference on Intelligent Robots and Systems, pp.2145-2150, 2008. ,
DOI : 10.1109/IROS.2008.4650993
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.506.496
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://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.278.7587
Randomized tree construction algorithm to explore energy landscapes, Journal of Computational Chemistry, vol.319, issue.16, pp.3464-3474, 2011. ,
DOI : 10.1016/S0009-2614(00)00081-6
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.589.7111
Fast marching tree: A fast marching sampling-based method for optimal motion planning in many dimensions, The International Journal of Robotics Research, vol.20, issue.4, pp.883-921, 2015. ,
DOI : 10.1109/MRA.2013.2248309
De Novo Computational Design of Retro-Aldol Enzymes, Science, vol.37, issue.90001, pp.1387-1391, 2008. ,
DOI : 10.1093/nar/gkh028
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431203
De novo protein design using pairwise potentials and a genetic algorithm, Protein Science, vol.206, issue.4, pp.567-574, 1994. ,
DOI : 10.1080/07391102.1991.10507882
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2142856
Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen, Journal of Molecular Biology, vol.267, issue.3, pp.727-748, 1997. ,
DOI : 10.1006/jmbi.1996.0897
Incremental sampling-based algorithms for optimal motion planning, Robotics Science and Systems VI, vol.104, 2010. ,
Sampling-based algorithms for optimal motion planning, The International Journal of Robotics Research, vol.23, issue.7, pp.846-894, 2011. ,
DOI : 10.1109/TRO.2006.886840
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://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.19.3462
A united residue force-field for calcium-protein interactions, Protein Science, vol.37, issue.10, pp.2725-2735, 2004. ,
DOI : 10.1007/s002140050399
An NMA-guided path planning approach for computing large-amplitude conformational changes in proteins, Proteins: Structure, Function, and Bioinformatics, vol.33, issue.1, pp.131-143, 2007. ,
DOI : 10.1007/978-1-4615-4022-9
Optimization by Simulated Annealing, Science, vol.220, issue.4598, pp.671-680, 1983. ,
DOI : 10.1126/science.220.4598.671
Monte carlo simulations of protein folding. I. Lattice model and interaction scheme, Proteins: Structure, Function, and Genetics, vol.3, issue.4, pp.338-352, 1994. ,
DOI : 10.1007/978-3-642-82803-4
The development/application of a 'minimalist' organic/biochemical molecular mechanic force field using a combination of ab initio calculations and experimental data, 1997. ,
Computer Simulation of Biomolecular Systems, numéro 3 de Computer Simulations of Biomolecular Systems, pp.83-96, 1997. ,
Improved prediction of protein side-chain conformations with SCWRL4, Proteins: Structure, Function, and Bioinformatics, vol.77, issue.4, pp.778-795, 2009. ,
RRT-Connect: An efficient approach to single-query path planning, Proc. IEEE Int'l Conf. on Robotics and Automation, pp.995-1001, 2000. ,
Design of a Novel Globular Protein Fold with Atomic-Level Accuracy, Science, vol.302, issue.5649, pp.1364-1368, 2003. ,
DOI : 10.1126/science.1089427
Escaping free-energy minima, Proceedings of the National Academy of Sciences, vol.6, issue.4598, pp.12562-12566, 2002. ,
DOI : 10.1126/science.220.4598.671
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC130499
Robot Motion Planning, 1991. ,
DOI : 10.1007/978-1-4615-4022-9
Rapidly-Exploring Random Trees: A New Tool for Path Planning, 1998. ,
Rapidly-Exploring Random Trees: Progress and Prospects, Algorithmic and Computational Robotics: New Directions, pp.293-308, 2000. ,
Randomized Kinodynamic Planning, The International Journal of Robotics Research, vol.20, issue.5, pp.378-400, 2001. ,
Planning Algorithms, p.63, 2006. ,
Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm, Proteins: Structure, Function, and Bioinformatics, vol.33, issue.2, pp.227-239, 1998. ,
Displacement analysis of the general spatial 7-link 7R mechanism. Mechanism and Machine Theory, pp.219-226, 1988. ,
A new vector theory for the analysis of spatial mechanisms. Mechanism and Machine Theory, pp.209-217, 1988. ,
A critical evaluation of novel algorithms for the off-lattice Monte Carlo simulation of condensed polymer phases, Atomistic Modeling of Physical Properties, numéro 116 de Advances in Polymer Science, pp.283-318, 1994. ,
DOI : 10.1007/BFb0080202
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.32, issue.9, 2014. ,
DOI : 10.1177/0278364913488805
URL : http://arxiv.org/pdf/1407.2896
Incrementally reducing dispersion by increasing Voronoi bias in RRTs, IEEE International Conference on Robotics and Automation, 2004. Proceedings. ICRA '04. 2004, pp.3251-3257, 2004. ,
DOI : 10.1109/ROBOT.2004.1308755
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.80.2752
Progress in computational protein design, Current Opinion in Biotechnology, vol.18, issue.4, pp.305-311, 2007. ,
Tomas Lozano-Perez. Spatial planning: A configuration space approach, IEEE transactions on computers, vol.100, issue.2, pp.108-120, 1983. ,
Ary and Bassil I. Dahiyat. Development of a cytokine analog with enhanced stability using computational ultrahigh throughput screening, pp.1218-1226, 2002. ,
Backbone flexibility in computational protein design, Current Opinion in Biotechnology, vol.20, issue.4, pp.420-428, 2009. ,
Efficient inverse kinematics for general 6R manipulators, IEEE Transactions on Robotics and Automation, vol.10, issue.5, pp.648-657, 1994. ,
DOI : 10.1109/70.326569
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.35.9985
Kinematic Synthesis Antonson, editeurs, Formal Engineering Design Synthesis, p.63, 2001. ,
Optimal design of robots, Robotics: Science and Systems I, p.63, 2005. ,
DOI : 10.15607/RSS.2005.I.041
URL : https://hal.archives-ouvertes.fr/inria-00000473
Teller and Edward Teller. Equation of State Calculations by Fast Computing Machines, The Journal of Chemical Physics, vol.21, issue.93, pp.1087-1103, 1953. ,
Roadmap methods for protein folding, Methods in Molecular Biology, vol.413, issue.94, pp.219-239, 2008. ,
DOI : 10.1385/1-59745-574-1:219
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.299.3918
A probabilistic roadmap-based method to model conformational switching of a protein among many functionally-relevant structures, Intl Conf on Bioinf and Comp Biol (BI- CoB), pp.2014-2032, 2014. ,
The MARTINI Coarse-Grained Force Field: Extension to Proteins, Journal of Chemical Theory and Computation, vol.4, issue.5, pp.819-834, 2008. ,
DOI : 10.1021/ct700324x
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.456.7408
Contact pair dynamics during folding of two small proteins: Chicken villin head piece and the Alzheimer protein ??-amyloid, The Journal of Chemical Physics, vol.85, issue.3, pp.1602-1612, 2004. ,
DOI : 10.1063/1.1475756
Alteration of enzyme specificity by computational loop remodeling and design, Proceedings of the National Academy of Sciences, pp.9215-9220, 2009. ,
Structure of an Intermediate State in Protein Folding and Aggregation, Science, vol.73, issue.4, pp.362-366, 2012. ,
DOI : 10.1016/0092-8674(93)90259-S
Structure and energy landscape of a photoswitchable peptide: A replica exchange molecular dynamics study, Proteins: Structure, Function, and Bioinformatics, vol.119, issue.3, pp.485-494, 2005. ,
DOI : 10.1007/s008940100045
Multiscale Monte Carlo Sampling of Protein Sidechains: Application to Binding Pocket Flexibility, Journal of Chemical Theory and Computation, vol.4, issue.5, pp.835-846, 2008. ,
DOI : 10.1021/ct700334a
Monte Carlo Sampling with Hierarchical Move Sets: POSH Monte Carlo, Journal of Chemical Theory and Computation, vol.5, issue.8, pp.1968-1984, 2009. ,
DOI : 10.1021/ct8005166
Energy Landscape and Global Optimization for a Frustrated Model Protein, The Journal of Physical Chemistry B, vol.115, issue.39, pp.11525-11529, 2011. ,
Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations, Proceedings of the National Academy of Sciences, vol.81, issue.18, pp.11844-11849, 2006. ,
DOI : 10.1063/1.448118
THEORY OF PROTEIN FOLDING: The Energy Landscape Perspective, Annual Review of Physical Chemistry, vol.48, issue.1, pp.545-600, 1997. ,
DOI : 10.1146/annurev.physchem.48.1.545
Theory of protein folding, Current Opinion in Structural Biology, vol.14, issue.1, pp.70-75, 2004. ,
Application of a Molecular Dynamics Simulation Method with a Generalized Effective Potential to the Flexible Molecular Docking Problems, The Journal of Physical Chemistry B, vol.104, issue.2, pp.354-359, 2000. ,
DOI : 10.1021/jp993073h
Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent, The Journal of Chemical Physics, vol.126, issue.1, p.14903, 2007. ,
DOI : 10.1021/ct050196z
Conformational splitting: A more powerful criterion for dead-end elimination, Journal of Computational Chemistry, vol.9, issue.11, pp.999-1009, 2000. ,
DOI : 10.1002/1096-987X(200008)21:11<999::AID-JCC9>3.0.CO;2-A
Protein design is NP-hard, Protein engineering, vol.15, issue.96, pp.779-782, 2002. ,
Computational protein design with a generalized born solvent model: Application to asparaginyl-tRNA synthetase, Proteins: Structure, Function, and Bioinformatics, vol.13, issue.12, pp.3448-3468, 2011. ,
DOI : 10.1110/ps.03250104
URL : https://hal.archives-ouvertes.fr/hal-00764853
Tertiary templates for proteins, Journal of Molecular Biology, vol.193, issue.4, pp.775-791, 1987. ,
DOI : 10.1016/0022-2836(87)90358-5
Calcul des modèles géométriques inverses des robots manipulateurs 6R. Rapport technique 06332, LAAS, 2006. ,
An obstacle-based rapidly-exploring random tree, Proceedings 2006 IEEE International Conference on Robotics and Automation, 2006. ICRA 2006., 2006. ,
DOI : 10.1109/ROBOT.2006.1641823
Determination of reaction coordinates via locally scaled diffusion map, The Journal of chemical physics, vol.134, issue.12, pp.3-624, 2011. ,
Kemp elimination catalysts by computational enzyme design, Nature, vol.160, issue.7192, pp.190-195, 2008. ,
DOI : 10.1103/PhysRevB.37.785
Multi-Objective Design and Path Planning Optimization of Unmanned Aerial Vehicles (UAVs), Proc. 16th AIAA/ISSMO Multidisciplinary Analysis and Optimization Conference, pp.10-2514, 2015. ,
A Single-Query Bi-Directional Probabilistic Roadmap Planner with Lazy Collision Checking, Robotics Research, vol.6, pp.403-417, 2003. ,
DOI : 10.1007/3-540-36460-9_27
Folding free-energy landscape of a 10-residue mini-protein, chignolin, FEBS Letters, vol.113, issue.14, pp.3422-3426, 2006. ,
DOI : 10.1021/ja00025a002
Prediction, determination and validation of phase diagrams via the global study of energy landscapes, International Journal of Materials Research, vol.100, issue.2, pp.135-152, 2009. ,
Conformational Analysis of Macromolecules. II. The Rotational Isomeric States of the Normal Hydrocarbons, The Journal of Chemical Physics, vol.44, issue.8, p.3054, 1966. ,
Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction, Science, vol.329, issue.5989, pp.309-313, 2010. ,
Visibility-based probabilistic roadmaps for motion planning, Advanced Robotics, vol.14, issue.6, pp.477-493, 2000. ,
DOI : 10.1163/156855300741960
Manipulation Planning with Probabilistic Roadmaps, The International Journal of Robotics Research, vol.23, issue.7-8, pp.729-746, 2004. ,
DOI : 10.1177/027836499101000604
Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins, Proteins: Structure, Function, and Genetics, vol.5, issue.1, pp.82-95, 1999. ,
DOI : 10.1002/(SICI)1097-0134(19990101)34:1<82::AID-PROT7>3.0.CO;2-A
A motion planning approach to flexible ligand binding, Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology, pp.252-261, 1999. ,
Protein Misfolding and Neurodegeneration, Archives of Neurology, vol.65, issue.2, pp.184-189, 2008. ,
DOI : 10.1001/archneurol.2007.56
URL : http://archneur.jamanetwork.com/data/journals/neur/7514/nnr70011_184_189.pdf
Robot Modeling and Control, 2005. ,
Pareto optimization in computational protein design with multiple objectives, Journal of Computational Chemistry, vol.17, issue.16, pp.2704-2711, 2008. ,
DOI : 10.1017/CBO9780511626418
Challenges in the computational design of proteins, Journal of The Royal Society Interface, vol.307, issue.12, pp.477-491, 2009. ,
DOI : 10.1371/journal.pcbi.0020168
Using multi-objective computational design to extend protein promiscuity, Biophysical Chemistry, vol.147, issue.12, pp.13-19, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00765922
A Sampling-Based Tree Planner for Systems With Complex Dynamics, IEEE Transactions on Robotics, vol.28, issue.1, pp.116-131, 2012. ,
DOI : 10.1109/TRO.2011.2160466
Replica Monte Carlo Simulation of Spin-Glasses, Physical Review Letters, vol.57, issue.21, pp.2607-2609, 1986. ,
STUDIES ON PROTEIN FOLDING, UNFOLDING AND FLUCTUATIONS BY COMPUTER SIMULATION, International Journal of Peptide and Protein Research, vol.6, issue.6, pp.445-459, 1975. ,
DOI : 10.1111/j.1399-3011.1975.tb02446.x
Conformational change of proteins arising from normal mode calculations, Protein Engineering, Design and Selection, vol.14, issue.1, pp.1-6, 2001. ,
DOI : 10.1093/protein/14.1.1
A Global Geometric Framework for Nonlinear Dimensionality Reduction, Science, vol.290, issue.5500, pp.2319-2323, 2000. ,
Protein folding by motion planning, Physical Biology, vol.2, issue.4, pp.148-155, 2005. ,
DOI : 10.1088/1478-3975/2/4/S09
Simulating Protein Motions with Rigidity Analysis, Journal of Computational Biology, vol.14, issue.6, pp.839-855, 2007. ,
DOI : 10.1089/cmb.2007.R019
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.211.3555
Rigidity analysis for protein motion and folding core identification, Bibliography Proc. AAAI Workshop on Artificial Intelligence and Robotics Methods in Computational Biology, p.2013, 2013. ,
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling, Journal of Computational Physics, vol.23, issue.94, pp.187-199, 1977. ,
DOI : 10.1016/0021-9991(77)90121-8
A series of PDB-related databanks for everyday needs, Nucleic Acids Research, vol.43, issue.D1, pp.364-368, 2015. ,
DOI : 10.1093/nar/gku1028
Coarse-grained models for proteins, Current Opinion in Structural Biology, vol.15, issue.2, pp.144-150, 2005. ,
DOI : 10.1016/j.sbi.2005.02.005
A new framework for computational protein design through cost function network optimization, Bioinformatics, vol.29, issue.17, pp.2129-2136, 2013. ,
DOI : 10.1093/bioinformatics/btt374
Monte Carlo backbone sampling for polypeptides with variable bond angles and dihedral angles using concerted rotations and a Gaussian bias, The Journal of Chemical Physics, vol.118, issue.9, p.4261, 2003. ,
Polypeptide Folding Using Monte Carlo Sampling, Concerted Rotation, and Continuum Solvation, Journal of the American Chemical Society, vol.126, issue.6, pp.1849-1857, 2004. ,
Finding the lowest free energy conformation of a protein is an NP-hard problem: Proof and implications, Bulletin of Mathematical Biology, vol.245, issue.6, pp.1183-1198, 1993. ,
DOI : 10.6028/jres.094.010
Trading accuracy for speed: a quantitative comparison of search algorithms in protein sequence design 1 1Edited by J. Thornton, Journal of Molecular Biology, vol.299, issue.3, pp.789-803, 2000. ,
DOI : 10.1006/jmbi.2000.3758
Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms, The Journal of Physical Chemistry A, vol.101, issue.94, pp.5111-5116, 1997. ,
Automatic protein design with all atom force-fields by exact and heuristic optimization 1 1Edited by J. Thorton, Journal of Molecular Biology, vol.301, issue.3, pp.713-736, 2000. ,
DOI : 10.1006/jmbi.2000.3984
MAPRM: a probabilistic roadmap planner with sampling on the medial axis of the free space, Proceedings 1999 IEEE International Conference on Robotics and Automation (Cat. No.99CH36288C), pp.1024-1031, 1999. ,
DOI : 10.1109/ROBOT.1999.772448
Analytical Rebridging Monte Carlo: Application to cis/trans Isomerization in Proline-Containing, Cyclic Peptides, The Journal of Chemical Physics, vol.111, issue.14, p.6625, 1999. ,
Efficient Monte Carlo methods for cyclic peptides, Molecular Physics, vol.97, issue.34, pp.559-580, 1999. ,
Computational Design of Calmodulin Mutants with up to 900-Fold Increase in Binding Specificity, Journal of Molecular Biology, vol.385, issue.5, pp.1470-1480, 2009. ,
DOI : 10.1016/j.jmb.2008.09.053
A test of lattice protein folding algorithms, Proceedings of the National Academy of Sciences, pp.325-329, 1995. ,
Local energy landscape flattening: Parallel hyperbolic Monte Carlo sampling of protein folding, Proteins: Structure, Function, and Genetics, vol.22, issue.2, pp.192-201, 2002. ,
DOI : 10.1002/1096-987X(200102)22:3<339::AID-JCC1006>3.0.CO;2-R
Convergence of replica exchange molecular dynamics, The Journal of Chemical Physics, vol.81, issue.15, p.154105, 2005. ,
DOI : 10.1021/bi9704764
FAST Conformational Searches by Balancing Exploration/Exploitation Trade-Offs, Journal of Chemical Theory and Computation, 2015. ,