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Atomic Scale Determination of Enzyme Flexibility and Active Site Stability through Static Modes: Case of Dihydrofolate Reductase

 Marie Brut , Alain Estève , Georges Landa , Guillaume Renvez , Mehdi Djafari-Rouhani , et al.
Journal of Physical Chemistry B, 2011, 115 (7), pp.1616-1622. ⟨10.1021/jp109874z⟩
Article dans une revue hal-01481808v1
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MoMA-LigPath: A web server to simulate protein-ligand unbinding

 Didier Devaurs , Léa Bouard , Marc Vaisset , Christophe Zanon , Ibrahim Al Bluwi , et al.
Nucleic Acids Research, 2013, vol. 41, pp. 297-302. ⟨10.1093/nar/gkt380⟩
Article dans une revue hal-00843321v1
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MoMA-LoopSampler: A web server to exhaustively sample protein loop conformations

 Amélie Barozet , Kevin Molloy , Marc Vaisset , Christophe Zanon , Pierre Fauret , et al.
Bioinformatics, 2022, 38 (2), pp.552-553. ⟨10.1093/bioinformatics/btab584⟩
Article dans une revue hal-03326493v1
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Simultaneous System Design and Path Planning: A Sampling-based Algorithm.

 Kevin Molloy , Laurent Denarie , Marc Vaisset , Thierry Simeon , Juan Cortés
The International Journal of Robotics Research, 2019, 38 (2-3), pp.375-387. ⟨10.1177/0278364918783054⟩
Article dans une revue hal-01834414v1
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A multi-tree approach to compute transition paths on energy landscapes

 Didier Devaurs , Marc Vaisset , Thierry Simeon , Juan Cortés
Workshop on Artificial Intelligence and Robotics Methods in Computational Biology, AAAI '13, Jul 2013, Bellevue, United States. pp. 8-13
Communication dans un congrès hal-00872247v1
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Predicting secondary structure propensities in IDPs using simple statistics from three-residue fragments

 Alejandro N Estaña , Amélie Barozet , Assia Mouhand , Marc Vaisset , Christophe Zanon , et al.
Journal of Molecular Biology, 2020, 342 (19), pp.5447-5459. ⟨10.1016/j.jmb.2020.07.026⟩
Article dans une revue hal-02920302v1
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Combining System Design and Path Planning

 Laurent Denarie , Kevin Molloy , Marc Vaisset , Thierry Simeon , Juan Cortés
Goldberg K., Abbeel P., Bekris K., Miller L. Algorithmic Foundations of Robotics XII, 13, , pp.112-127, 2020, Springer Proceedings in Advanced Robotics, ⟨10.1007/978-3-030-43089-4_8⟩
Chapitre d'ouvrage hal-02571707v1
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Segmenting Proteins into Tripeptides to Enhance Conformational Sampling with Monte Carlo Methods

 Laurent Denarie , Ibrahim Al Bluwi , Marc Vaisset , Thierry Simeon , Juan Cortés
Molecules, 2018, 23 (2), pp.373. ⟨10.3390/molecules23020373⟩
Article dans une revue hal-01708710v1
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Coarse-grained elastic networks, normal mode analysis and robotics-inspired methods for modeling protein conformational transitions

 Ibrahim Al Bluwi , Marc Vaisset , Thierry Simeon , Juan Cortés
IEEE International Conference on Bioinformatics and Biomedicine Workshops, Oct 2012, Philadelphia, United States. pp.40-47, ⟨10.1109/BIBMW.2012.6470359⟩
Communication dans un congrès hal-01981799v1
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Modeling protein conformational transitions by a combination of coarse-grained normal mode analysis and robotics-inspired methods

 Ibrahim Al Bluwi , Marc Vaisset , Thierry Simeon , Juan Cortés
BMC Structural Biology, 2013, 13 (Suppl 1), pp.S2. ⟨10.1186/1472-6807-13-S1-S2⟩
Article dans une revue hal-01980925v1
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Combining System Design and Path Planning

 Laurent Denarie , Kevin Molloy , Marc Vaisset , Thierry Simeon , Juan Cortés
Workshop on the Algorithmic Foundations of Robotics (WAFR), Dec 2016, San Francisco, United States
Communication dans un congrès hal-01364042v1
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Exhaustive exploration of the conformational landscape of small cyclic peptides using a robotics approach

 Maud Jusot , Dirk Stratmann , Marc Vaisset , Jacques Chomilier , Juan Cortés
Journal of Chemical Information and Modeling, 2018, 58 (11), pp.2355-2368. ⟨10.1021/acs.jcim.8b00375⟩
Article dans une revue hal-01893751v1
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A Reinforcement Learning Approach to Protein Loop Modeling

 Kevin Molloy , Nicolas Buhours , Marc Vaisset , Thierry Simeon , Étienne Ferré , et al.
IEEE/RSJ International Conference on Intelligent Robots and Systems, Sep 2015, Hamburg, Germany
Communication dans un congrès hal-01206128v1
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Characterizing Energy Landscapes of Peptides using a Combination of Stochastic Algorithms

 Didier Devaurs , Kevin Molloy , Marc Vaisset , Amarda Shehu , Thierry Simeon , et al.
IEEE Transactions on NanoBioscience, 2015, 14 (5), pp. 545-552
Article dans une revue hal-01143833v1
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Protein loops with multiple meta-stable conformations: a challenge for sampling and scoring methods

 Amélie Barozet , Marc Bianciotto , Marc Vaisset , Thierry Simeon , Hervé Minoux , et al.
Proteins - Structure, Function and Bioinformatics, 2021, 89 (2), pp.218-231. ⟨10.1002/prot.26008⟩
Article dans une revue hal-02947409v1
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Hybrid parallelization of a multi-tree path search algorithm: Application to highly-flexible biomolecules

 Alejandro N Estaña , Kevin Molloy , Marc Vaisset , Nathalie Sibille , Thierry Simeon , et al.
Parallel Computing, 2018, 77, pp.84-100. ⟨10.1016/j.parco.2018.06.005⟩
Article dans une revue hal-01823694v2
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Realistic Ensemble Models of Intrinsically Disordered Proteins Using a Structure-Encoding Coil Database

 Alejandro N Estaña , Nathalie Sibille , Elise Delaforge , Marc Vaisset , Juan Cortés , et al.
Structure, 2019, 27 (5), pp.381-391.e2. ⟨10.1016/j.str.2018.10.016⟩
Article dans une revue hal-01954977v1
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A Reinforcement-Learning-Based Approach to Enhance Exhaustive Protein Loop Sampling

 Amélie Barozet , Kevin Molloy , Marc Vaisset , Thierry Simeon , Juan Cortés
Bioinformatics, 2020, 36 (4), pp.1099-1106. ⟨10.1093/bioinformatics/btz684⟩
Article dans une revue hal-02289207v1

Deformation of thiolated nucleic acid deposited on a silicon surface: A Static Mode approach

 Marie Brut , Alain Estève , Georges Landa , Guillaume Renvez , Mehdi Djafari-Rouhani , et al.
Materials Science and Engineering: B, 2010, 169 (1-3), pp.23-27. ⟨10.1016/j.mseb.2009.11.014⟩
Article dans une revue istex hal-01481814v1
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