40 3.2.1 Dynamic Clash-avoiding Constraints, p.42 ,
71 5.2.1 Elimination of dominated strategies, p.74 ,
74 5.2.2.1 Logit map properties, p.76 ,
94 6.2.1 -dynamic and -equilibrium, 96 6.2.2.1 Asymptotic pseudo trajectory . . . . . . . . . . . . 96 6.2.2.2 Global convergence with the continuous dynamics 97 ,
Non-coding RNA, Human Molecular Genetics, vol.15, issue.suppl_1, pp.17-29, 2006. ,
DOI : 10.1093/hmg/ddl046
The classification of amino acid conservation, Journal of Theoretical Biology, vol.119, issue.2, pp.205-218, 1986. ,
DOI : 10.1016/S0022-5193(86)80075-3
Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid, Nature, vol.9, issue.4356, pp.737-738, 1953. ,
DOI : 10.1016/0006-3002(53)90232-7
The discovery of the ?-helix and ?-sheet, the principal structural features of proteins, pp.11-207, 2003. ,
The structure of proteins: Two hydrogen-bonded helical configurations of the polypeptide chain, Proceedings of the National Academy of Sciences, vol.203, issue.4, pp.205-211, 1951. ,
DOI : 10.1021/cr60102a002
The PyMOL Molecular Graphics System, Version 1.8 Schrödinger, LLC, 2016. ,
Cis peptide bonds in proteins: residues involved, their conformations, interactions and locations 1 1Edited by J. M. Thornton, Journal of Molecular Biology, vol.294, issue.1, pp.271-288, 1999. ,
DOI : 10.1006/jmbi.1999.3217
Stereochemistry of polypeptide chain configurations, Journal of Molecular Biology, vol.7, issue.1, pp.95-99, 1963. ,
DOI : 10.1016/S0022-2836(63)80023-6
Conformation of Polypeptides and Proteins, Advances in Protein Chemistry, vol.23, pp.283-437, 1968. ,
DOI : 10.1016/S0065-3233(08)60402-7
A series of PDB related databases for everyday needs, Nucleic Acids Research, vol.39, issue.Database, pp.411-419, 2011. ,
DOI : 10.1093/nar/gkq1105
The PSIPRED protein structure prediction server, Bioinformatics, vol.16, issue.4, pp.404-405, 2000. ,
DOI : 10.1093/bioinformatics/16.4.404
Prediction of protein secondary structure by the hidden Markov model, Bioinformatics, vol.9, issue.2, pp.141-146, 1993. ,
DOI : 10.1093/bioinformatics/9.2.141
Free energy calculation of modified base-pair formation in explicit solvent: A predictive model, RNA, vol.15, issue.12, pp.2278-2287, 2009. ,
DOI : 10.1261/rna.1734309
Codon???anticodon pairing: The wobble hypothesis, Journal of Molecular Biology, vol.19, issue.2, pp.548-555, 1966. ,
DOI : 10.1016/S0022-2836(66)80022-0
URL : http://profiles.nlm.nih.gov/SC/B/C/B/S/_/scbcbs.pdf
VARNA: Interactive drawing and editing of the RNA secondary structure, Bioinformatics, vol.25, issue.15, pp.1974-1979, 2009. ,
DOI : 10.1093/bioinformatics/btp250
URL : https://hal.archives-ouvertes.fr/hal-00432548
Tools for the automatic identification and classification of RNA base pairs, Nucleic Acids Research, vol.31, issue.13, pp.3450-3460, 2003. ,
DOI : 10.1093/nar/gkg529
Geometric nomenclature and classification of RNA base pairs, RNA, vol.7, issue.4, pp.499-512, 2001. ,
DOI : 10.1017/S1355838201002515
Algorithms for Loop Matchings, SIAM Journal on Applied Mathematics, vol.35, issue.1, pp.68-82, 1978. ,
DOI : 10.1137/0135006
RNA Pseudoknot Prediction in Energy-Based Models, Journal of Computational Biology, vol.7, issue.3-4, pp.409-427, 2000. ,
DOI : 10.1089/106652700750050862
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information, Nucleic Acids Research, vol.9, issue.1, pp.133-148, 1981. ,
DOI : 10.1093/nar/9.1.133
URL : https://academic.oup.com/nar/article-pdf/9/1/133/6201945/9-1-133.pdf
Predicting RNA secondary structures from sequence and probing data, Methods, vol.103, pp.86-98, 2016. ,
DOI : 10.1016/j.ymeth.2016.04.004
URL : https://hal.archives-ouvertes.fr/hal-01393649
Prediction of RNA secondary structure by free energy minimization, Current Opinion in Structural Biology, vol.16, issue.3, pp.270-278, 2006. ,
DOI : 10.1016/j.sbi.2006.05.010
An RNA folding method capable of identifying pseudoknots and base triples, Bioinformatics, vol.14, issue.8, pp.691-699, 1998. ,
DOI : 10.1093/bioinformatics/14.8.691
Three-dimensional protein structure prediction: Methods and computational strategies, Computational Biology and Chemistry, vol.53, pp.251-276, 2014. ,
DOI : 10.1016/j.compbiolchem.2014.10.001
Analysis of Four-Way Junctions in RNA Structures, Journal of Molecular Biology, vol.390, issue.3, pp.547-559, 2009. ,
DOI : 10.1016/j.jmb.2009.04.084
Topology of three-way junctions in folded RNAs, RNA, vol.12, issue.1, pp.83-93, 2006. ,
DOI : 10.1261/rna.2208106
URL : https://hal.archives-ouvertes.fr/hal-00094313
Automated motif extraction and classification in RNA tertiary structures, RNA, vol.14, issue.12, pp.2489-2497, 2008. ,
DOI : 10.1261/rna.1061108
URL : https://hal.archives-ouvertes.fr/hal-00353402
Correlation of observed fold frequency with the occurrence of local structural motifs, Journal of Molecular Biology, vol.287, issue.5, pp.969-981, 1999. ,
DOI : 10.1006/jmbi.1999.2642
The CATH protein family database: A resource for structural and functional annotation of genomes, PROTEOMICS, vol.28, issue.1, pp.11-21, 2002. ,
DOI : 10.1110/ps.8.4.699
SCOP: A structural classification of proteins database for the investigation of sequences and structures, Journal of Molecular Biology, vol.247, issue.4, pp.536-540, 1995. ,
DOI : 10.1016/S0022-2836(05)80134-2
The Pfam protein families database: towards a more sustainable future, Nucleic Acids Research, vol.44, issue.D1, pp.279-285, 2016. ,
DOI : 10.1093/nar/gkv1344
URL : https://hal.archives-ouvertes.fr/hal-01294685
The Protein Data Bank, Nucleic Acids Research, vol.28, issue.1, pp.235-242, 2000. ,
DOI : 10.1093/nar/28.1.235
URL : http://journals.iucr.org/d/issues/2002/06/01/an0594/an0594.pdf
Protein???Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations, Journal of Molecular Biology, vol.331, issue.1, pp.281-299, 2003. ,
DOI : 10.1016/S0022-2836(03)00670-3
Prediction of protein interaction sites from sequence profile and residue neighbor list, Proteins: Structure, Function, and Genetics, vol.271, issue.3, pp.336-343, 2001. ,
DOI : 10.1006/jmbi.1997.1198
Recent Progress and Future Directions in Protein-Protein Docking, Current Protein & Peptide Science, vol.9, issue.1, pp.1-15, 2008. ,
DOI : 10.2174/138920308783565741
URL : https://hal.archives-ouvertes.fr/inria-00434268
Assessing Structural Predictions of Protein-Protein Recognition: The CAPRI Experiment, Reviews in Computational Chemistry, vol.60, issue.Web Server issu, pp.137-173, 2015. ,
DOI : 10.1002/prot.20551
Critical assessment of methods of protein structure prediction: Progress and new directions in round XI, en, Proteins, pp.4-14, 2016. ,
DOI : 10.1093/nar/gkt294
Introduction to protein crystallization, pp.254-265, 2004. ,
An Introduction to Biological NMR Spectroscopy, Molecular & Cellular Proteomics, vol.8, issue.11, pp.3006-3025, 2013. ,
DOI : 10.1016/j.jmb.2007.07.008
URL : https://hal.archives-ouvertes.fr/hal-01321578
A Consensus on Protein Structure Accuracy in NMR?, Structure, vol.23, issue.2, pp.255-256, 2015. ,
DOI : 10.1016/j.str.2015.01.007
How cryo-EM is revolutionizing structural biology, Trends in Biochemical Sciences, vol.40, issue.1, pp.49-57, 2015. ,
DOI : 10.1016/j.tibs.2014.10.005
The revolution will not be crystallized: a new method sweeps through structural biology, Nature, vol.525, issue.7568, p.172, 2015. ,
DOI : 10.1038/525172a
URL : http://www.nature.com:80/polopoly_fs/1.18335!/menu/main/topColumns/topLeftColumn/pdf/525172a.pdf
RNA Structure Determination Using SAXS Data, The Journal of Physical Chemistry B, vol.114, issue.31, pp.1520-6106, 1021. ,
DOI : 10.1021/jp1057308
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3164809/pdf
Correlation Map, a goodnessof-fit test for one-dimensional X-ray scattering spectra, pp.419-422, 2015. ,
DOI : 10.1038/nmeth.3358
UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches, Bioinformatics, vol.31, issue.6, pp.926-932, 2015. ,
DOI : 10.1093/bioinformatics/btu739
URL : https://academic.oup.com/bioinformatics/article-pdf/31/6/926/569379/btu739.pdf
Principles that Govern the Folding of Protein Chains, Science, vol.181, issue.4096, pp.223-230, 1973. ,
DOI : 10.1126/science.181.4096.223
Perspective: Coarse-grained models for biomolecular systems, The Journal of Chemical Physics, vol.1, issue.9, pp.9-201, 2013. ,
DOI : 10.1063/1.3464776
URL : http://aip.scitation.org/doi/pdf/10.1063/1.4818908
Structure prediction for CASP8 with all-atom refinement using Rosetta, Proteins, pp.89-99, 2009. ,
DOI : 10.1002/(SICI)1097-0134(1999)37:3+<22::AID-PROT5>3.0.CO;2-W
URL : http://onlinelibrary.wiley.com/doi/10.1002/prot.22540/pdf
Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models, Journal of Chemical Theory and Computation, vol.10, issue.2, pp.676-690, 2014. ,
DOI : 10.1021/ct400617g
Using known substructures in protein model building and crystallography, pp.819-822, 1986. ,
GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies, PLOS ONE, vol.19, issue.4, pp.1932-6203, 2015. ,
DOI : 10.1371/journal.pone.0136444.s025
URL : https://hal.archives-ouvertes.fr/hal-01201665
Assessing the utility of coevolutionbased residue?residue contact predictions in a sequence-and structure-rich era, Proc Natl Acad Sci U S A, vol.110, issue.39, pp.15-674, 2013. ,
Toward High-Resolution de Novo Structure Prediction for Small Proteins, Science, vol.309, issue.5742, pp.1868-1871, 2005. ,
DOI : 10.1126/science.1113801
Development and testing of a general amber force field, Journal of Computational Chemistry, vol.17, issue.9, pp.1157-1174, 2004. ,
DOI : 10.1002/jcc.20035
CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields, Journal of Computational Chemistry, vol.249, issue.4, pp.671-690, 2010. ,
DOI : 10.1002/jcc.21367
Molecular dynamics simulations in biology, Nature, vol.347, issue.6294, pp.631-639, 1990. ,
DOI : 10.1038/347631a0
Dynamic personalities of proteins, Nature, vol.124, issue.7172, pp.964-972, 2007. ,
DOI : 10.1038/nature06522
Statistical mechanics: theory and molecular simulation, 2010. ,
Normal mode analysis and applications in biological physics, Journal of Physics: Condensed Matter, vol.22, issue.42, pp.953-8984, 2010. ,
DOI : 10.1088/0953-8984/22/42/423202
Rapidly-exploring random trees: Progress and prospects, 2000. ,
Motion planning algorithms for molecular simulations: A survey, Computer Science Review, vol.6, issue.4, pp.125-143, 2012. ,
DOI : 10.1016/j.cosrev.2012.07.002
Sampling-based exploration of folded state of a protein under kinematic and geometric constraints, Proteins: Structure, Function, and Bioinformatics, vol.126, issue.2, pp.25-43, 2012. ,
DOI : 10.1063/1.2740261
A multi-tree approach to compute transition paths on energy landscapes, Workshop on Artificial Intelligence and Robotics Methods in Computational Biology, AAAI'13, p.8, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00872247
Frustration-guided motion planning reveals conformational transitions in proteins, Proteins: Structure, Function, and Bioinformatics, vol.25, issue.10, 2017. ,
DOI : 10.1016/j.str.2016.12.003
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
iMod: multipurpose normal mode analysis in internal coordinates, Bioinformatics, vol.27, issue.20, pp.2843-2850, 2011. ,
DOI : 10.1093/bioinformatics/btr497
Modeling and design by hierarchical natural moves, Proceedings of the National Academy of Sciences, vol.682, issue.4, pp.2890-2895, 2012. ,
DOI : 10.1002/1097-0282(2000)56:4<275::AID-BIP10024>3.0.CO;2-E
URL : http://www.pnas.org/content/109/8/2890.full.pdf
Theory of games and economic behavior, 1947. ,
Algorithmic game theory, 2007. ,
DOI : 10.1017/CBO9780511800481
Game Theory Explorer: software for the applied game theorist, Computational Management Science, vol.70, issue.1, pp.5-33, 2015. ,
DOI : 10.1111/1468-0262.00300
URL : http://arxiv.org/pdf/1403.3969.pdf
No-regret dynamics and fictitious play, Journal of Economic Theory, vol.148, issue.2, pp.825-842, 2013. ,
DOI : 10.1016/j.jet.2012.07.003
URL : https://hal.archives-ouvertes.fr/hal-00713871
Subjectivity and correlation in randomized strategies, Journal of Mathematical Economics, vol.1, issue.1, pp.67-96, 1974. ,
DOI : 10.1016/0304-4068(74)90037-8
URL : http://www.ma.huji.ac.il/~raumann/pdf/Subjectivity and Correlation.pdf
Regret in the On-Line Decision Problem, Games and Economic Behavior, vol.29, issue.1-2, pp.7-35, 1999. ,
DOI : 10.1006/game.1999.0740
A Simple Adaptive Procedure Leading to Correlated Equilibrium, pp.1127-1150, 2000. ,
DOI : 10.1111/1468-0262.00153
URL : http://www.dklevine.com/archive/refs4572.pdf
Approximation to Bayes risk in repeated play, Contributions to the Theory of Games, pp.97-139, 1957. ,
DOI : 10.1515/9781400882151-006
Regret Analysis of Stochastic and Nonstochastic Multi-armed Bandit Problems, Foundations and Trends?? in Machine Learning, vol.5, issue.1, pp.1-122, 2012. ,
DOI : 10.1561/2200000024
URL : http://arxiv.org/pdf/1204.5721.pdf
Using confidence bounds for exploitation-exploration trade-offs, Journal of Machine Learning Research, vol.3, pp.397-422, 2002. ,
Adaptive Game Playing Using Multiplicative Weights, Games and Economic Behavior, vol.29, issue.1-2, pp.79-103, 1999. ,
DOI : 10.1006/game.1999.0738
URL : http://www.cs.princeton.edu/~schapire/papers/FreundScYY.pdf
The Weighted Majority Algorithm, Information and Computation, vol.108, issue.2, pp.212-261, 1994. ,
DOI : 10.1006/inco.1994.1009
URL : https://doi.org/10.1006/inco.1994.1009
Fast, Clash-Free RNA Conformational Morphing using Molecular Junctions, Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics , ACM-BCB '17, 2017. ,
DOI : 10.1145/3107411.3107460
Real-space protein-model completion: an inverse-kinematics approach, Acta Crystallographica Section D Biological Crystallography, vol.61, issue.1, pp.2-13, 2005. ,
DOI : 10.1107/S0907444904025697
Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.5, issue.4, pp.534-545, 2008. ,
DOI : 10.1109/TCBB.2008.96
Geometric analysis characterizes molecular rigidity in generic and non-generic protein configurations, Journal of the Mechanics and Physics of Solids, vol.83, pp.36-47, 2015. ,
DOI : 10.1016/j.jmps.2015.06.006
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4509548/pdf
Characterizing RNA ensembles from NMR data with kinematic models, Nucleic Acids Research, vol.42, issue.15, 2014. ,
DOI : 10.1093/nar/gku707
URL : https://hal.archives-ouvertes.fr/hal-01058971
Protocols for Molecular Modeling with Rosetta3 and RosettaScripts, Biochemistry, vol.55, issue.34, pp.4748-4763, 2016. ,
DOI : 10.1021/acs.biochem.6b00444
URL : http://doi.org/10.1021/acs.biochem.6b00444
Biopython: freely available Python tools for computational molecular biology and bioinformatics, Bioinformatics, vol.25, issue.11, pp.1422-1423, 2009. ,
DOI : 10.1093/bioinformatics/btp163
URL : https://academic.oup.com/bioinformatics/article-pdf/25/11/1422/944180/btp163.pdf
Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch, Cell Reports, vol.13, issue.9, pp.1800-1813, 2015. ,
DOI : 10.1016/j.celrep.2015.10.062
DSSR: an integrated software tool for dissecting the spatial structure of RNA, Nucleic Acids Research, vol.43, issue.21, pp.142-142, 2015. ,
DOI : 10.1093/nar/gkv716
Riboswitches as versatile gene control elements, Current Opinion in Structural Biology, vol.15, issue.3, pp.342-348, 2005. ,
DOI : 10.1016/j.sbi.2005.05.003
Bacterial aptamers that selectively bind glutamine, RNA Biology, vol.276, issue.1, pp.82-89, 2011. ,
DOI : 10.1261/rna.7214405
URL : http://www.tandfonline.com/doi/pdf/10.4161/rna.8.1.13864?needAccess=true
Structural basis for nucleotide exchange in heterotrimeric G proteins, Science, vol.286, issue.5, pp.1361-1365, 2015. ,
DOI : 10.1074/jbc.M110.190496
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4968074/pdf
Hybridizing rapidly exploring random trees and basin hopping yields an improved exploration of energy landscapes, Journal of Computational Chemistry, vol.124, issue.8, pp.739-752, 2016. ,
DOI : 10.1063/1.2148958
URL : https://hal.archives-ouvertes.fr/hal-01497994
Targeting RNA with Small Molecules, Chemical Reviews, vol.108, issue.4, pp.1171-1224, 2008. ,
DOI : 10.1021/cr0681546
Topology Links RNA Secondary Structure with Global Conformation, Dynamics, and Adaptation, Science, vol.312, issue.5777, pp.202-206, 2010. ,
DOI : 10.1126/science.1128451
Is one solution good enough?, Nature Structural & Molecular Biology, vol.10, issue.3, pp.184-185, 1038. ,
DOI : 10.1002/ijch.199400022
Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers, Acta Crystallographica Section D Biological Crystallography, vol.65, issue.10, pp.1107-1117, 2009. ,
DOI : 10.1107/S0907444909030613
The clipper project, Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, vol.40, 2002. ,
V12. 1: User's Manual for CPLEX, International Business Machines Corporation, vol.46, issue.53, p.157, 2009. ,
Martingale limit theory and its application, en, 1980. ,
On Information and Sufficiency, The Annals of Mathematical Statistics, vol.22, issue.1, pp.79-86, 1951. ,
DOI : 10.1214/aoms/1177729694
URL : http://doi.org/10.1214/aoms/1177729694
Population games and evolutionary dynamics, 2010. ,
Higher order game dynamics, Journal of Economic Theory, vol.148, issue.6, pp.2666-2695, 2013. ,
DOI : 10.1016/j.jet.2013.08.002
URL : https://hal.archives-ouvertes.fr/hal-01382303
Convex analysis, ser. Princeton Landmarks in Mathematics, 1970. ,
Online Learning and Online Convex Optimization, Machine Learning, pp.107-194, 2012. ,
DOI : 10.1561/2200000018
Learning in Games via Reinforcement and Regularization, Mathematics of Operations Research, vol.41, issue.4, pp.1297-1324, 2016. ,
DOI : 10.1287/moor.2016.0778
URL : https://hal.archives-ouvertes.fr/hal-01382286
Dynamics of stochastic approximation algorithms, Seminaire de probabilites XXXIII, pp.1-68, 1999. ,
DOI : 10.1007/978-1-4757-1947-5
Oddness of the number of equilibrium points: A new proof, International Journal of Game Theory, vol.21, issue.1, pp.235-250, 1973. ,
DOI : 10.1007/BF01737572
Scilab: Free and Open Source software for numerical computation, Scilab Enterprises, p.3, 2012. ,
Evolution in games with randomly disturbed payoffs, Journal of Economic Theory, vol.132, issue.1, pp.47-69, 2007. ,
DOI : 10.1016/j.jet.2005.05.011
URL : http://www.ssc.wisc.edu/%7Ewhs/research/rdp.pdf
Refinement of protein conformations using a macromolecular energy minimization procedure, Journal of Molecular Biology, vol.46, issue.2, pp.269-2790022, 1969. ,
DOI : 10.1016/0022-2836(69)90421-5
PISCES: a protein sequence culling server, Bioinformatics, vol.19, issue.12, pp.1589-1591, 2003. ,
DOI : 10.1093/bioinformatics/btg224
URL : https://academic.oup.com/bioinformatics/article-pdf/19/12/1589/718266/btg224.pdf
SIFT: predicting amino acid changes that affect protein function, Nucleic Acids Research, vol.31, issue.13, pp.3812-3814, 2003. ,
DOI : 10.1093/nar/gkg509
URL : https://academic.oup.com/nar/article-pdf/31/13/3812/9487105/gkg509.pdf
A Reinforcement Learning Approach to Protein Loop Modeling, IEEE/RSJ International Conference on Intelligent Robots and Systems, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01206128
Fast protein fragment similarity scoring using a Binet???Cauchy kernel, Bioinformatics, vol.30, issue.6, pp.784-791, 2014. ,
DOI : 10.1093/bioinformatics/btt618
URL : https://academic.oup.com/bioinformatics/article-pdf/30/6/784/17345719/btt618.pdf