Molecular Motion Algorithms

González-Delgado Javier, González-Sanz Alberto, Cortés Juan, Neuvial Pierre. 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, doi: 10.1214/23-EJS2135, hal_id: hal-03369795 Elena-Real Carlos, Urbanek Annika, Lund Xamuel, Morató Anna, Sagar Amin, Fournet Aurélie, Estaña Alejandro, Bellande Tracy, Allemand Frédéric, Cortés Juan, Sibille Nathalie, Melki Ronald, Bernadó Pau. Multi-site-specific isotopic labeling accelerates high-resolution structural investigations of pathogenic huntingtin exon-1, Structure, , 2023, doi: 10.1016/j.str.2023.04.003, hal_id: hal-04085383 González-Delgado Javier, Sagar Amin, Zanon Christophe, Lindorff-Larsen Kresten, Bernadó Pau, Neuvial Pierre, Cortés Juan. WASCO: A Wasserstein-based Statistical Tool to Compare Conformational Ensembles of Intrinsically Disordered Proteins, Journal of Molecular Biology, 168053, 2023, doi: 10.1016/j.jmb.2023.168053, hal_id: hal-04056662 Elena-Real Carlos A, Sagar Amin, Urbanek Annika, Popovic Matija, Morató Anna, Estaña Alejandro, Fournet Aurélie, Doucet Christine, Lund Xamuel L, Shi Zhen-Dan, Costa Luca, Thureau Aurélien, Allemand Frédéric, Swenson Rolf E, Milhiet Pierre-Emmanuel, Crehuet Ramon, Barducci Alessandro, Cortés Juan, Sinnaeve Davy, Sibille Nathalie, Bernadó Pau. The structure of pathogenic huntingtin exon 1 defines the bases of its aggregation propensity, Nature Structural and Molecular Biology, 30(3): 309 - 320, 2023, doi: 10.1038/s41594-023-00920-0, hal_id: hal-04052774 Mier Pablo, Elena-Real Carlos, Cortés Juan, Bernadó Pau, Andrade-Navarro Miguel. The sequence context in poly-alanine regions: structure, function and conservation, Bioinformatics, 38(21): 4851--4858, 2022, doi: 10.1093/bioinformatics/btac610, hal_id: hal-03778766 González-Delgado Javier, Bernadó Pau, Neuvial Pierre, Cortés Juan. Statistical proofs of the interdependence between nearest neighbor effects on polypeptide backbone conformations, Journal of Structural Biology, 214(4): 107907, 2022, doi: 10.1016/j.jsb.2022.107907, hal_id: hal-03826233 Gonçalves-Kulik Mariane, Mier Pablo, Kastano Kristina, Cortés Juan, Bernadó Pau, Schmid Friederike, Andrade-Navarro Miguel. Low Complexity Induces Structure in Protein Regions Predicted as Intrinsically Disordered, Biomolecules, 12(8): 1098, 2022, doi: 10.3390/biom12081098, hal_id: hal-03767342 González-Foutel Nicolás, Glavina Juliana, Borcherds Wade, Safranchik Matías, Barrera-Vilarmau Susana, Sagar Amin, Estaña Alejandro, Barozet Amelie, Garrone Nicolás, Fernandez-Ballester Gregorio, Blanes-Mira Clara, Sánchez Ignacio, de Prat-Gay Gonzalo, Cortés Juan, Bernadó Pau, Pappu Rohit, Holehouse Alex, Daughdrill Gary, Chemes Luc\á. Conformational buffering underlies functional selection in intrinsically disordered protein regions, Nature Structural and Molecular Biology, 29(8): 781-790, 2022, doi: 10.1038/s41594-022-00811-w, hal_id: hal-03767337 Barozet Amélie, Molloy Kevin, Vaisset Marc, Zanon Christophe, Fauret Pierre, Siméon Thierry, Cortés Juan. MoMA-LoopSampler: A web server to exhaustively sample protein loop conformations, Bioinformatics, 38(2): 552--553, 2022, doi: 10.1093/bioinformatics/btab584, hal_id: hal-03326493 Barozet Amélie, Chacón Pablo, Cortés Juan. Current approaches to flexible loop modeling, Current Research in Structural Biology, 3: 187-191, 2021, doi: 10.1016/j.crstbi.2021.07.002, hal_id: hal-03318652 Clerc Ilinka, Sagar Amin, Barducci Alessandro, Sibille Nathalie, Bernadó Pau, Cortés Juan. The diversity of molecular interactions involving intrinsically disordered proteins: A molecular modeling perspective, Computational and Structural Biotechnology Journal, 19: 3817-3828, 2021, doi: 10.1016/j.csbj.2021.06.031, hal_id: hal-03281983 Bouchiba Younes, Cortés Juan, Schiex Thomas, Barbe Sophie. Molecular flexibility in computational protein design: an algorithmic perspective, Protein Engineering, Design and Selection, 34: gzab011, 2021, doi: 10.1093/protein/gzab011, hal_id: hal-03221838 Pelus Angeline, Bordes Gaëlle, Barbe Sophie, Bouchiba Younes, Burnard Callum , Cortés Juan, Enjalbert Brice, Esque Jeremy, Estaña Alejandro, Fauré Régis, Henras Anthony K, Heux Stephanie, Le Men Claude, Millard Pierre, Nouaille Sébastien, Pérochon Julien, Toanen Marion, Truan Gilles, Verdier Amandine, Wagner Camille, Romeo Yves, Montanier Cédric Y. A tripartite carbohydrate-binding module to functionalize cellulose nanocrystal, Biomaterials Science, 9(22): 7444-7455, 2021, doi: 10.1039/d1bm01156a, hal_id: hal-03372120 A. Barozet, M. Bianciotto, M. Vaisset, T. Siméon, H. Minoux, J. Cortés. Protein loops with multiple meta-stable conformations: a challenge for sampling and scoring methods, Proteins - Structure, Function and Bioinformatics, 89(2): 218-231, 2021, doi: 10.1002/prot.26008, hal_id: hal-02947409 T. Joshi, S. Garg, A. Estaña, J. Cortés, P. Bernadó, S. Das, A.R. Kammath, A. Sagar, S. Rakshit. Interdomain linkers tailor the stability of immunoglobulin repeats in polyproteins, Biochemical and Biophysical Research Communications, 550: 43-48, 2021, doi: 10.1016/j.bbrc.2021.02.114, hal_id: hal-03161535 A. Estaña, A. Barozet, A. Mouhand, M Vaisset, C. Zanon, P. Fauret, N. Sibille, P. Bernadó, J. Cortés. Predicting secondary structure propensities in IDPs using simple statistics from three-residue fragments, Journal of Molecular Biology, 432(19): 5447-5459, 2020, doi: 10.1016/j.jmb.2020.07.026, hal_id: hal-02920302 A. Urbanek, M. Popovic, A. Morató, A. Estaña, C. Elena-Real, P. Mier, A. Fournet, F. Allemand, S. Delbecq, M. Andrade-Navarro, J. Cortés, N. Sibille, P. Bernadó. Flanking regions determine the structure of the poly-glutamine homo- repeat in huntingtin through mechanisms common among glutamine-rich human proteins, Structure, 28(7): 733-746.e5, 2020, doi: 10.1016/j.str.2020.04.008, hal_id: hal-02893075 A. Urbanek, M. Popovic, C. Elena-Real, A. Morató, A. Estaña, A. Fournet, F. Allemand, A.M. Gil, C. Cativiela, J. Cortés, A.I. Jiménez, N. Sibille, P. Bernadó. Evidence of the reduced abundance of proline cis conformation in protein poly-proline tracts, Journal of the American Chemical Society, 142(17): 7976--7986, 2020, doi: 10.1021/jacs.0c02263, hal_id: hal-02545935 A. Barozet, K. Molloy, M. Vaisset, T. Siméon, J. Cortés. A reinforcement-learning-based approach to enhance exhaustive protein loop sampling, Bioinformatics, 36(4): 1099-1106, 2020, doi: 10.1093/bioinformatics/btz684, hal_id: hal-02289207 S. Abb, N. Tarrat, J. Cortés, B. Andriyevsky, L. Harnau, J.C. Schön, S. Rauschenbach, K. Kern. Carbohydrate self-assembly at surfaces: STM imaging of sucrose conformation and ordering on Cu(100), Angewandte Chemie International Edition, 58(25): 8336-8340, 2019, doi: 10.1002/anie.201901340, hal_id: hal-02146428 S. Abb, N. Tarrat, J. Cortés, B. Andriyevsky, L. Harnau, J.C. Schön, S. Rauschenbach, K. Kern. Polymorphism in carbohydrate self-assembly at surfaces: STM imaging and theoretical modelling of trehalose on Cu(100), RSC Advances, 9(61): 35813-35819, 2019, doi: 10.1039/C9RA06764G, hal_id: hal-02370437 A. Charpentier, D. Mignon, S. Barbe, J. Cortés, T. Schiex, T. Simonson, D. Allouche. Variable neighborhood search with cost function networks to solve large computational protein design problems, Journal of Chemical Information and Modeling, 59(1): 127-136, 2019, doi: 10.1021/acs.jcim.8b00510, hal_id: hal-01943616 A. Estaña, M. Ghallab, P. Bernadó, J. Cortés. Investigating the formation of structural elements in proteins using local sequence-dependent information and a heuristic search algorithm, Molecules, 24(6): 1150, 2019, doi: 10.3390/molecules24061150, hal_id: hal-02080026 K. Molloy, L. Denarie, M. Vaisset, T. Siméon, J. Cortés. Simultaneous system design and path planning: a sampling-based algorithm., The International Journal of Robotics Research, 38(2-3): 375-387, 2019, doi: 10.1177/0278364918783054, hal_id: hal-01834414 A. Estaña, N. Sibille, E. Delaforge, M. Vaisset, J. Cortés, P. Bernadó. Realistic ensemble models of intrinsically disordered proteins using a structure-encoding coil database, Structure, 27(5): 381-391.e2, 2019, doi: 10.1016/j.str.2018.10.016, hal_id: hal-01954977 A. Estaña, K. Molloy, M. Vaisset, N. Sibille, T. Siméon, P. Bernadó, J. Cortés. Hybrid parallelization of a multi-tree path search algorithm: Application to highly-flexible biomolecules, Parallel Computing, 77: 84-100, 2018, doi: 10.1016/j.parco.2018.06.005, hal_id: hal-01823694 L. Denarie, I. Al-Bluwi, M. Vaisset, T. Siméon, J. Cortés. Segmenting proteins into tripeptides to enhance conformational sampling with Monte Carlo methods, Molecules, 23(2): 373, 2018, doi: 10.3390/molecules23020373, hal_id: hal-01708710 A. Barozet, M. Bianciotto, T. Siméon, H. Minoux, J. Cortés. Conformational changes in antibody Fab fragments upon binding and their consequences on the performance of docking algorithms, Immunology Letters, 200: 5-15, 2018, doi: 10.1016/j.imlet.2018.06.002, hal_id: hal-01823695 M. Jusot, D. Stratmann, M. Vaisset, J. Chomilier, J. Cortés. Exhaustive exploration of the conformational landscape of small cyclic peptides using a robotics approach, Journal of Chemical Information and Modeling, 58(11): 2355-2368, 2018, doi: 10.1021/acs.jcim.8b00375, hal_id: hal-01893751 T.N. Cordeiro, F. Herranz-Trillo, A. Urbanek, A. Estaña, J. Cortés, N. Sibille, P. Bernadó. Structural characterization of highly flexible proteins by small-angle scattering, Advances in Experimental Medicine and Biology, 107-129, 2017, doi: 10.1007/978-981-10-6038-0_7, hal_id: hal-01664316 J.C. Schön, C. Oligschleger, J. Cortés. Prediction and clarification of structures of (bio)molecules on surfaces-a review, Zeitschrift für Naturforschung, B : Chemical Sciences, 71(5): 352-374, 2016, doi: 10.1515/znb-2015-0222, hal_id: hal-01295377 L. Tapia, J. Cortés, A. Shehu, J. Chen. Foreword on special issue on robotics methods for structural and dynamic modeling of molecular systems, Robotica, 34(08): 1677-1678, 2016, doi: 10.1017/S0263574716000370, hal_id: hal-01942773 D. Devaurs, K. Molloy, M. Vaisset, A. Shehu, T. Siméon, J. Cortés. Characterizing energy landscapes of peptides using a combination of stochastic algorithms, IEEE Transactions on NanoBioscience, 14(5): 545-552, 2015, doi: 10.1109/TNB.2015.2424597, hal_id: hal-01143833 D. Devaurs, L. Bouard, M. Vaisset, C. Zanon, I. Al-Bluwi, R. Iehl, T. Siméon, J. Cortés. MoMA-LigPath: A web server to simulate protein-ligand unbinding, Nucleic Acids Research, 41: 297-302, 2013, doi: 10.1093/nar/gkt380, hal_id: hal-00843321 I. Al-Bluwi, T. Siméon, J. Cortés. Motion planning algorithms for molecular simulations: A survey, Computer Science Review, 6(4): 125-143, 2012, doi: 10.1016/j.cosrev.2012.07.002, hal_id: hal-01982596 G. Paës, J. Cortés, T. Siméon, M. O'Donohue, V. Tran. Thumb-loops up for catalysis: a structure/function investigation of a functional loop movement in a GH11 xylanase, Computational and Structural Biotechnology Journal, 1(2): e201207001, 2012, doi: 10.5936/csbj.201207001, hal_id: hal-01267831 L. Jaillet, F.J. Corcho, J.J. Pérez, J. Cortés. A randomized tree construction algorithm to explore energy landscapes, Journal of Computational Chemistry, 32(16): 3464-3474, 2011, doi: 10.1002/jcc.21931, hal_id: hal-01894030 Y. Li, J. Cortés, T. Siméon. Enhancing systematic protein-protein docking methods using ray casting: Application to ATTRACT, Proteins - Structure, Function and Bioinformatics, 79(11): 3037-3049, 2011, doi: 10.1002/prot.23127, hal_id: hal-01982609 S. Barbe, J. Cortés, T. Siméon, P. Monsan, M. Remaud-Siméon, I. André. A mixed molecular modeling-robotics approach to investigate lipase large molecular motions, Proteins - Structure, Function and Bioinformatics, 79(8): 2517-2529, 2011, doi: 10.1002/prot.23075, hal_id: hal-01982630 J. Cortés, S. Barbe, M. Erard, T. Siméon. Encoding molecular motions in voxel maps, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8(2): 557-563, 2011, doi: 10.1109/TCBB.2010.23, hal_id: hal-01985823 J. Cortés, D.T. Le, R. Iehl, T. Siméon. Simulating ligand-induced conformational changes in proteins using a mechanical disassembly method, Physical Chemistry Chemical Physics, 12(29): 8268-8276, 2010, doi: 10.1039/C002811H, hal_id: hal-01986237 V. Lafaquière, S. Barbe, S. Puech-Guenot, D. Guieysse, J. Cortés, P. Monsan, T. Siméon, I. André, M. Remaud-Siméon. Control of lipase enantioselectivity by engineering the substrate binding site and access channel, ChemBioChem, 10(17): 2760-2771, 2009, doi: 10.1002/cbic.200900439, hal_id: hal-01986285 S. Kirillova, J. Cortés, A. Stefaniu, T. Siméon. An NMA-guided path planning approach for computing large-amplitude conformational changes in proteins, Proteins - Structure, Function and Bioinformatics, 70(1): 131-143, 2008, doi: 10.1002/prot.21570, hal_id: hal-01987938 J. Cortés, T. Siméon, V. Ruiz-de-Angulo, D. Guieysse, M. Remaud-Siméon, V. Tran. A path planning approach for computing large-amplitude motions of flexible molecules, Bioinformatics, 21(Suppl 1): i116-i125, 2005, doi: 10.1093/bioinformatics/bti1017, hal_id: hal-01988625 J. Cortés, T. Siméon, M. Remaud-Siméon, V. Tran. Geometric algorithms for the conformational analysis of long protein loops, Journal of Computational Chemistry, 25(7): 956-967, 2004, doi: 0.1002/jcc.20021, hal_id: hal-01987902