2024

Journal articles

Valentin Milia, Nathalie Tarrat, Christophe Zanon, Juan Cortés, Mathias Rapacioli. Exploring Molecular Energy Landscapes by Coupling the DFTB Potential with a Tree-Based Stochastic Algorithm: Investigation of the Conformational Diversity of Phthalates. Journal of Chemical Information and Modeling, 2024, 64 (8), pp.3290-3301. ⟨10.1021/acs.jcim.3c01981⟩. ⟨hal-04517230⟩

Simon Wasiela, Marco Cognetti, Paolo Robuffo Giordano, Juan Cortés, Thierry Simeon. Robust Motion Planning with Accuracy Optimization based on Learned Sensitivity Metrics. IEEE Robotics and Automation Letters, In press. ⟨hal-04636547⟩

Nathalie Tarrat, J. Christian Schön, Juan Cortés. Dependence of lactose adsorption on the exposed crystal facets of metals: a comparative study of gold, silver and copper. Physical Chemistry Chemical Physics, 2024, 31, pp.21134-21146. ⟨10.1039/D4CP01559B⟩. ⟨hal-04664324⟩

Conference papers

Simon Wasiela, Smail Ait Bouhsain, Marco Cognetti, Juan Cortés, Thierry Simeon. Learned Uncertainty Tubes via Recurrent Neural Networks for Planning Robust Robot Motions. 27th European Conference on Artificial Intelligence (ECAI), Oct 2024, Santiago de Compostela, Spain. ⟨hal-04636454⟩

Other documents

Simon Wasiela, Marco Cognetti, Paolo Robuffo Giordano, Juan Cortés, Thierry Simeon. Robust Motion Planning and Accuracy Optimization based on Learned Sensitivity Metric (Video). 2024. ⟨hal-04642257⟩

Preprints, Working Papers, ...

Simon Wasiela, Smail Ait Bouhsain, Marco Cognetti, Juan Cortés, Thierry Simeon. Note on learning sensitivity metrics for a quadrotor. 2024. ⟨hal-04642304⟩

2023

Journal articles

William Margerit, Antoine Charpentier, Cathy Maugis-Rabusseau, Johann Christian Schön, Nathalie Tarrat, et al.. IGLOO: An Iterative Global Exploration and Local Optimization Algorithm to Find Diverse Low-Energy Conformations of Flexible Molecules. Algorithms, 2023, 16 (10), pp.476. ⟨10.3390/a16100476⟩. ⟨hal-04247201⟩

Enrica Rossi, Marco Tognon, Luca Ballotta, Ruggero Carli, Juan Cortés, et al.. Coordinated Multi-Robot Trajectory Tracking Control over Sampled Communication ⋆. Automatica, 2023, 151, pp.110941. ⟨10.1016/j.automatica.2023.110941⟩. ⟨hal-04010855⟩

Carlos Elena-Real, Annika Urbanek, Xamuel Lund, Anna Morató, Amin Sagar, et al.. Multi-site-specific isotopic labeling accelerates high-resolution structural investigations of pathogenic huntingtin exon-1. Structure, 2023, 31 (6), pp.644-650.e5. ⟨10.1016/j.str.2023.04.003⟩. ⟨hal-04085383⟩

Carlos A Elena-Real, Amin Sagar, Annika Urbanek, Matija Popovic, Anna Morató, et al.. The structure of pathogenic huntingtin exon 1 defines the bases of its aggregation propensity. Nature Structural and Molecular Biology, 2023, 30 (3), pp.309 - 320. ⟨10.1038/s41594-023-00920-0⟩. ⟨hal-04052774⟩

Javier González-Delgado, Alberto González-Sanz, Juan Cortés, Pierre Neuvial. Two-sample goodness-of-fit tests on the flat torus based on Wasserstein distance and their relevance to structural biology. Electronic Journal of Statistics , 2023, 17 (1), pp.1547-1586. ⟨10.1214/23-EJS2135⟩. ⟨hal-03369795v3⟩

Javier González-Delgado, Amin Sagar, Christophe Zanon, Kresten Lindorff-Larsen, Pau Bernadó, et al.. WASCO: A Wasserstein-based Statistical Tool to Compare Conformational Ensembles of Intrinsically Disordered Proteins. Journal of Molecular Biology, 2023, 435 (14), pp.168053. ⟨10.1016/j.jmb.2023.168053⟩. ⟨hal-04056662⟩

Conference papers

Simon Wasiela, Paolo Robuffo Giordano, Juan Cortés, Thierry Simeon. A Sensitivity-Aware Motion Planner (SAMP) to Generate Intrinsically-Robust Trajectories. IEEE International Conference on Robotics and Automation (ICRA), 2023, London, United Kingdom. ⟨hal-03808933v2⟩

Preprints, Working Papers, ...

Javier González-Delgado, Juan Cortés, Pierre Neuvial. Post-clustering Inference under Dependency. 2023. ⟨hal-04250364⟩

Simon Wasiela, Marco Cognetti, Paolo Robuffo Giordano, Juan Cortés, Thierry Simeon. Learned Sensitivity Metrics for Robust and Accurate Motion Planning. 2023. ⟨hal-04027078⟩

2022

Journal articles

Amélie Barozet, Kevin Molloy, Marc Vaisset, Christophe Zanon, Pierre Fauret, et al.. MoMA-LoopSampler: A web server to exhaustively sample protein loop conformations. Bioinformatics, 2022, 38 (2), pp.552-553. ⟨10.1093/bioinformatics/btab584⟩. ⟨hal-03326493⟩

Mariane Gonçalves-Kulik, Pablo Mier, Kristina Kastano, Juan Cortés, Pau Bernadó, et al.. Low Complexity Induces Structure in Protein Regions Predicted as Intrinsically Disordered. Biomolecules, 2022, 12 (8), pp.1098. ⟨10.3390/biom12081098⟩. ⟨hal-03767342⟩

Pablo Mier, Carlos Elena-Real, Juan Cortés, Pau Bernadó, Miguel Andrade-Navarro. The sequence context in poly-alanine regions: structure, function and conservation. Bioinformatics, 2022, 38 (21), pp.4851-4858. ⟨10.1093/bioinformatics/btac610⟩. ⟨hal-03778766⟩

A E Jiménez-Cano, Dario Sanalitro, M. Tognon, A. Franchi, J. Cortés. Precise Cable-Suspended Pick-and-Place with an Aerial Multi-robot System. Journal of Intelligent and Robotic Systems, 2022, 105 (3), pp.68. ⟨10.1007/s10846-022-01668-3⟩. ⟨hal-03748086⟩

Javier González-Delgado, Pau Bernadó, Pierre Neuvial, Juan Cortés. Statistical proofs of the interdependence between nearest neighbor effects on polypeptide backbone conformations. Journal of Structural Biology, 2022, 214 (4), pp.107907. ⟨10.1016/j.jsb.2022.107907⟩. ⟨hal-03826233⟩

Bohdan Andriyevsky, Nathalie Tarrat, Juan Cortés, Johann Christian Schön. Dehydrogenation versus deprotonation of disaccharide molecules in vacuum: a thorough theoretical investigation. Royal Society Open Science, 2022, 9 (10), ⟨10.1098/rsos.220436⟩. ⟨hal-03817247⟩

Nicolás González-Foutel, Juliana Glavina, Wade Borcherds, Matías Safranchik, Susana Barrera-Vilarmau, et al.. Conformational buffering underlies functional selection in intrinsically disordered protein regions. Nature Structural and Molecular Biology, 2022, 29 (8), pp.781-790. ⟨10.1038/s41594-022-00811-w⟩. ⟨hal-03767337⟩

Dario Sanalitro, Marco Tognon, A Jimenez Cano, Juan Cortés, Antonio Franchi. Indirect Force Control of a Cable-suspended Aerial Multi-Robot Manipulator. IEEE Robotics and Automation Letters, 2022, 7 (3), pp.6726 - 6733. ⟨10.1109/LRA.2022.3176457⟩. ⟨hal-03664826⟩

Conference papers

Younes Bouchiba, Juan Cortés, Thomas Schiex, Sophie Barbe. Computational Design of miniprotein binders. Journées Scientifiques du GDR ChemBio, Jun 2022, Toulouse, France. ⟨hal-04223586⟩

2021

Journal articles

Angeline Pelus, Gaëlle Bordes, Sophie Barbe, Younes Bouchiba, Callum Burnard, et al.. A tripartite carbohydrate-binding module to functionalize cellulose nanocrystal. Biomaterials Science, 2021, 9 (22), pp.7444-7455. ⟨10.1039/d1bm01156a⟩. ⟨hal-03372120⟩

Tanuja Joshi, Surbhi Garg, Alejandro Estaña, Juan Cortés, Pau Bernadó, et al.. Interdomain linkers tailor the stability of immunoglobulin repeats in polyproteins. Biochemical and Biophysical Research Communications, 2021, 550, pp.43-48. ⟨10.1016/j.bbrc.2021.02.114⟩. ⟨hal-03161535⟩

Ilinka Clerc, Amin Sagar, Alessandro Barducci, Nathalie Sibille, Pau Bernadó, et al.. The diversity of molecular interactions involving intrinsically disordered proteins: A molecular modeling perspective. Computational and Structural Biotechnology Journal, 2021, 19, pp.3817-3828. ⟨10.1016/j.csbj.2021.06.031⟩. ⟨hal-03281983⟩

Amélie Barozet, Marc Bianciotto, Marc Vaisset, Thierry Simeon, Hervé Minoux, et al.. Protein loops with multiple meta-stable conformations: a challenge for sampling and scoring methods. Proteins - Structure, Function and Bioinformatics, 2021, 89 (2), pp.218-231. ⟨10.1002/prot.26008⟩. ⟨hal-02947409⟩

Amélie Barozet, Pablo Chacón, Juan Cortés. Current approaches to flexible loop modeling. Current Research in Structural Biology, 2021, 3, pp.187-191. ⟨10.1016/j.crstbi.2021.07.002⟩. ⟨hal-03318652⟩

Younes Bouchiba, Juan Cortés, Thomas Schiex, Sophie Barbe. Molecular flexibility in computational protein design: an algorithmic perspective. Protein Engineering, Design and Selection, 2021, 34, pp.gzab011. ⟨10.1093/protein/gzab011⟩. ⟨hal-03221838⟩

Book sections

Juan Cortés, Thierry Simeon. Sampling-Based Tree Planners (RRT, EST, and Variations). Encyclopedia of Robotics, Springer Berlin Heidelberg, pp.1-9, 2021, ⟨10.1007/978-3-642-41610-1_170-1⟩. ⟨hal-03165054⟩

Conference papers

Younes Bouchiba, Manon Ruffini, Juan Cortés, Thomas Schiex, Sophie Barbe. Computational Design of miniprotein binders. GGMM 2021, Sep 2021, Villeneuve d’Ascq, France. ⟨hal-04223596⟩

2020

Journal articles

Dario Sanalitro, Heitor J Savino, Marco Tognon, Juan Cortés, Antonio Franchi. Full-pose Manipulation Control of a Cable-suspended load with Multiple UAVs under Uncertainties. IEEE Robotics and Automation Letters, 2020, 5 (2), pp.2185 - 2191. ⟨10.1109/LRA.2020.2969930⟩. ⟨hal-02460422⟩

Annika N Urbanek, Matija Popovic, Anna Morató, Alejandro N Estaña, Carlos A Elena-Real, et al.. Flanking regions determine the structure of the poly-glutamine homo- repeat in huntingtin through mechanisms common among glutamine-rich human proteins. Structure, 2020, 28 (7), pp.733-746.e5. ⟨10.1016/j.str.2020.04.008⟩. ⟨hal-02893075⟩

Alejandro N Estaña, Amélie Barozet, Assia Mouhand, Marc Vaisset, Christophe Zanon, et al.. Predicting secondary structure propensities in IDPs using simple statistics from three-residue fragments. Journal of Molecular Biology, 2020, 342 (19), pp.5447-5459. ⟨10.1016/j.jmb.2020.07.026⟩. ⟨hal-02920302⟩

Annika N Urbanek, Matija Popovic, Carlos A Elena-Real, Anna Morató, Alejandro N Estaña, et al.. Evidence of the reduced abundance of proline cis conformation in protein poly-proline tracts. Journal of the American Chemical Society, 2020, 142 (17), pp.7976-7986. ⟨10.1021/jacs.0c02263⟩. ⟨hal-02545935⟩

Amélie Barozet, Kevin Molloy, Marc Vaisset, Thierry Simeon, Juan Cortés. A Reinforcement-Learning-Based Approach to Enhance Exhaustive Protein Loop Sampling. Bioinformatics, 2020, 36 (4), pp.1099-1106. ⟨10.1093/bioinformatics/btz684⟩. ⟨hal-02289207⟩

Juan Cortés, Thomas Schiex. Aide à la conception. Le petit illustré, regards croisés de chercheur.es, 2020. ⟨hal-03436420⟩

Enrica Rossi, Marco Tognon, Ruggero Carli, Luca Schenato, Juan Cortés, et al.. Cooperative Aerial Load Transportation via Sampled Communication. IEEE Control Systems Letters, 2020, 4 (2), pp.277-282. ⟨10.1109/LCSYS.2019.2924413⟩. ⟨hal-02170909⟩

Book sections

Laurent Denarie, Kevin Molloy, Marc Vaisset, Thierry Simeon, Juan Cortés. Combining System Design and Path Planning. 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⟩. ⟨hal-02571707⟩

2019

Journal articles

Marco Tognon, Hermes A Tello Chávez, Enrico Gasparin, Quentin Sablé, Davide Bicego, et al.. A Truly Redundant Aerial Manipulator System with Application to Push-and-Slide Inspection in Industrial Plants. IEEE Robotics and Automation Letters, 2019, 4 (2), pp.1846 - 1851. ⟨10.1109/LRA.2019.2895880⟩. ⟨hal-01910343v2⟩

Alejandro N Estaña, Malik Ghallab, Pau Bernadó, Juan Cortés. Investigating the Formation of Structural Elements in Proteins Using Local Sequence-Dependent Information and a Heuristic Search Algorithm. Molecules, 2019, 24 (6), pp.1150. ⟨10.3390/molecules24061150⟩. ⟨hal-02080026⟩

Sabine Abb, Nathalie Tarrat, Juan Cortés, Bohdan Andriyevsky, Ludger Harnau, et al.. Carbohydrate Self-Assembly at Surfaces: STM Imaging of Sucrose Conformation and Ordering on Cu(100). Angewandte Chemie International Edition, 2019, 58 (25), pp.8336-8340. ⟨10.1002/anie.201901340⟩. ⟨hal-02146428⟩

Sabine Abb, Nathalie Tarrat, Juan Cortés, Bohdan Andriyevsky, Ludger Harnau, et al.. Polymorphism in carbohydrate self-assembly at surfaces: STM imaging and theoretical modelling of trehalose on Cu(100). RSC Advances, 2019, 9 (61), pp.35813-35819. ⟨10.1039/C9RA06764G⟩. ⟨hal-02370437⟩

Alejandro N Estaña, Nathalie Sibille, Elise Delaforge, Marc Vaisset, Juan Cortés, et al.. Realistic Ensemble Models of Intrinsically Disordered Proteins Using a Structure-Encoding Coil Database. Structure, 2019, 27 (5), pp.381-391.e2. ⟨10.1016/j.str.2018.10.016⟩. ⟨hal-01954977⟩

Kevin Molloy, Laurent Denarie, Marc Vaisset, Thierry Simeon, Juan Cortés. Simultaneous System Design and Path Planning: A Sampling-based Algorithm.. The International Journal of Robotics Research, 2019, 38 (2-3), pp.375-387. ⟨10.1177/0278364918783054⟩. ⟨hal-01834414⟩

Antoine Charpentier, David Mignon, Sophie Barbe, Juan Cortés, Thomas Schiex, et al.. Variable Neighborhood Search with Cost Function Networks To Solve Large Computational Protein Design Problems. Journal of Chemical Information and Modeling, 2019, 59 (1), pp.127-136. ⟨10.1021/acs.jcim.8b00510⟩. ⟨hal-01943616⟩

Book sections

Raphaël Lallement, Juan Cortés, Mamoun Gharbi, Alexandre Boeuf, Rachid Alami, et al.. Combining Assembly Planning and Geometric Task Planning. Anibal Ollero; Bruno Siciliano. Aerial Robotic Manipulation. Research, Development and Applications, 129, Springer, pp.299-316, 2019, Springer Tracts in Advanced Robotics, 978-3-030-12945-3. ⟨10.1007/978-3-030-12945-3_22⟩. ⟨hal-02191294⟩

Alexandre Boeuf, Juan Cortés, Thierry Simeon. Motion Planning. Aerial Robotic Manipulation, pp.317-332, 2019, 978-3-030-12945-3. ⟨10.1007/978-3-030-12945-3_23⟩. ⟨hal-02191300⟩

Conference papers

Yoann Solana, Hector Herrero Cueva, Alvaro Rubio Garcia, Sergio Martinez Calvo, Urko Esnaola Campos, et al.. A case study of automated dual-arm manipulation in industrial applications. 24th IEEE International Conference on Emerging Technologies and Factory Automation (ETFA 2019), Sep 2019, Zaragoza, Spain. pp.563-570, ⟨10.1109/ETFA.2019.8869209⟩. ⟨hal-02327826⟩

2018

Journal articles

Marco Tognon, Elisabetta Cataldi, Hermes Amadeus A Tello Chavez, Gianluca Antonelli, Juan Cortés, et al.. Control-Aware Motion Planning for Task-Constrained Aerial Manipulation. IEEE Robotics and Automation Letters, 2018, 3 (3), pp.2478-2484. ⟨10.1109/LRA.2018.2803206⟩. ⟨hal-01704127⟩

Alejandro N Estaña, Kevin Molloy, Marc Vaisset, Nathalie Sibille, Thierry Simeon, et al.. Hybrid parallelization of a multi-tree path search algorithm: Application to highly-flexible biomolecules. Parallel Computing, 2018, 77, pp.84-100. ⟨10.1016/j.parco.2018.06.005⟩. ⟨hal-01823694v2⟩

Maud Jusot, Dirk Stratmann, Marc Vaisset, Jacques Chomilier, Juan Cortés. Exhaustive exploration of the conformational landscape of small cyclic peptides using a robotics approach. Journal of Chemical Information and Modeling, 2018, 58 (11), pp.2355-2368. ⟨10.1021/acs.jcim.8b00375⟩. ⟨hal-01893751⟩

C. Schön,, C. Oligschleger, Juan Cortés. Prediction and clarification of structures of (bio)molecules on surfaces-a review . Zeitschrift fur Naturforschung B, 2018, 71 (5), ⟨10.1515/znb-2015-0222⟩. ⟨hal-01295377⟩

Laurent Denarie, Ibrahim Al Bluwi, Marc Vaisset, Thierry Simeon, Juan Cortés. Segmenting Proteins into Tripeptides to Enhance Conformational Sampling with Monte Carlo Methods. Molecules, 2018, 23 (2), pp.373. ⟨10.3390/molecules23020373⟩. ⟨hal-01708710⟩

Amélie Barozet, Marc Bianciotto, Thierry Simeon, Hervé Minoux, Juan Cortés. Conformational changes in antibody Fab fragments upon binding and their consequences on the performance of docking algorithms. Immunology Letters, 2018, 200, pp.5-15. ⟨10.1016/j.imlet.2018.06.002⟩. ⟨hal-01823695⟩

Anibal Ollero, Guillermo Heredia, Antonio Franchi, Gianluca Antonelli, Konstantin Kondak, et al.. The AEROARMS Project: Aerial Robots with Advanced Manipulation Capabilities for Inspection and Maintenance. IEEE Robotics and Automation Magazine, 2018, 25 (4), pp.12-23. ⟨10.1109/MRA.2018.2852789⟩. ⟨hal-01870107⟩

2017

Journal articles

Tiago N Cordeiro, Fatima Herranz-Trillo, Annika N Urbanek, Alejandro N Estaña, Juan Cortés, et al.. Structural Characterization of Highly Flexible Proteins by Small-Angle Scattering.. Advances in Experimental Medicine and Biology, 2017, pp.PP.107-129. ⟨10.1007/978-981-10-6038-0_7⟩. ⟨hal-01664316⟩

Tiago N Cordeiro, Fatima Herranz-Trillo, Annika N Urbanek, Alejandro N Estaña, Juan Cortés, et al.. Small-angle scattering studies of intrinsically disordered proteins and their complexes. Current Opinion in Structural Biology, 2017, 42, pp.15 - 23. ⟨10.1016/j.sbi.2016.10.011⟩. ⟨hal-01391541⟩

Conference papers

Yoann Solana, Michele Furci, Juan Cortés, Antonio Franchi. Multi-Robot Path Planning with Maintenance of Generalized Connectivity. 2017 IEEE 1st International Symposium on Multi-Robot and Multi-Agent Systems, Dec 2017, Los Angeles, United States. ⟨hal-01658557⟩

2016

Journal articles

Lydia Tapia, Juan Cortés, Amarda Shehu, Jinalin Chen. Foreword on special issue on robotics methods for structural and dynamic modeling of molecular systems. Robotica, 2016, 34 (08), pp.1677-1678. ⟨10.1017/S0263574716000370⟩. ⟨hal-01942773⟩

Didier Devaurs, Thierry Simeon, Juan Cortés. Optimal Path Planning in Complex Cost Spaces With Sampling-Based Algorithms. IEEE Transactions on Automation Science and Engineering, 2016, 13 (2), pp.415-424. ⟨10.1109/TASE.2015.2487881⟩. ⟨hal-01231482⟩

Conference papers

Laurent Denarie, Kevin Molloy, Marc Vaisset, Thierry Simeon, Juan Cortés. Combining System Design and Path Planning. Workshop on the Algorithmic Foundations of Robotics (WAFR), Dec 2016, San Francisco, United States. ⟨hal-01364042⟩

2015

Journal articles

Didier Devaurs, Kevin Molloy, Marc Vaisset, Amarda Shehu, Thierry Simeon, et al.. Characterizing Energy Landscapes of Peptides using a Combination of Stochastic Algorithms. IEEE Transactions on NanoBioscience, 2015, 14 (5), pp. 545-552. ⟨hal-01143833⟩

Conference papers

Alexandre Boeuf, Juan Cortés, Rachid Alami, Thierry Simeon. Enhancing sampling-based kinodynamic motion planning for quadrotors. IEEE/RSJ International Conference on Intelligent Robots and Systems, Sep 2015, Hamburg, Germany. ⟨hal-01231717⟩

Kevin Molloy, Nicolas Buhours, Marc Vaisset, Thierry Simeon, Étienne Ferré, et al.. A Reinforcement Learning Approach to Protein Loop Modeling. IEEE/RSJ International Conference on Intelligent Robots and Systems, Sep 2015, Hamburg, Germany. ⟨hal-01206128⟩

2014

Conference papers

Alexandre Boeuf, Juan Cortés, Rachid Alami, Thierry Simeon. Planning agile motions for quadrotors in constrained environments. IEEE/RSJ International Conference on Intelligent Robots and Systems, Sep 2014, Chicago, United States. 6p., ⟨10.1109/IROS.2014.6942564⟩. ⟨hal-01187138⟩

Didier Devaurs, Thierry Simeon, Juan Cortés. Efficient sampling-based approaches to optimal path planning in complex cost spaces. International Workshop on the Algorithmic Foundations of Robotics (WAFR), Aug 2014, Istanbul, Turkey. pp.16. ⟨hal-01062970⟩

Didier Devaurs, Amarda Shehu, Thierry Simeon, Juan Cortés. Sampling-based methods for a full characterization of energy landscapes of small peptides. IEEE International Conference on Bioinformatics and Biomedicine, Nov 2014, Belfast, United Kingdom. 8 p. ⟨hal-01070405⟩

Didier Devaurs, Thierry Simeon, Juan Cortés. A multi-tree extension of the Transition-based RRT: Application to ordering-and-pathfinding problems in continuous cost spaces. IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS), Sep 2014, Chicago, United States. 6 p. ⟨hal-01057030⟩

PhD thesis, HDR

Juan Cortés. Algorithmics of motion: From robotics, through structural biology, toward atomic-scale CAD. Robotics [cs.RO]. Universite Toulouse III Paul Sabatier, 2014. ⟨tel-01110545⟩