Publications
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2013. Modeling macromolecular complexes: a journey across scales. Modeling in Computational Biology and Biomedicine: A Multidisciplinary Endeavor.
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2015. Conformational ensembles and sampled landscapes: analysis and comparison. J. Comp. Chem.. 36:1213–31.
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2014. INRIA Tech Report: Conformational ensembles and sampled landscapes: analysis and comparison..
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2013. Towards Morse theory for point cloud data.. Inria Tech Reports.
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2011. Electrostatically–driven fast association and perdeuteration allow transferred cross–relaxation detection for G protein–coupled receptor ligands with equilibrium dissociation constants in the high–to–low nanomolar range. J Biomolecular Nmr. 50:191–5.
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2017. A Computational Methodology to Overcome the Challenges Associated With the Search for Specific Enzyme Targets to Develop Drugs Against.. Bioinform Biol Insights. 11:1177932217712471.
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2003. Extending the structure of an ABC transporter to atomic resolution: Modeling and simulation studies of MsbA. Biochemistry. 42:3666–3673.
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2013. A gating mechanism of pentameric ligand-gated ion channels. Proc. Natl. Acad. Sci. U.s.a.. 110:E3987–3996.
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2008. Does water condense in hydrophobic cavities? A molecular simulation study of hydration in heterogeneous nanopores J. Phys. Chem. C. 112:10435–10445.
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2023. Unwrapping NPT Simulations to Calculate Diffusion Coefficients. Journal of Chemical Theory and Computation. 19:3406–3417.
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2014. Type VI secretion and bacteriophage tail tubes share a common assembly pathway.. Embo Rep.. 15:315–21.
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2007. Water clustering and percolation in low hydration DNA shells. J. Phys. Chem. B. 111:3258–3266.
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2006. Water percolation governs polymorphic transitions and conductivity of DNA. Phys. Rev. Lett.. 97:137801.
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2008. Ion dynamics and water percolation effects in DNA polymorphism. J. Am. Chem. Soc.. 130:121–131.
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1998. Folding and Aggregation of Designed Protein Chains. Proc. Natl. Acad. Sci. Usa. 95:12930–1293.
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2005. Hydration and thermodynamic equilibrium of non-ionic surfactant in solution. Coll Surf A. 261:93–99.
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2010. Multiple binding sites for the general anesthetic isoflurane identified in the nicotinic acetylcholine receptor transmembrane domain.. Proc. Natl. Acad. Sci. U.s.a.. 107:14122–14127.
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2008. Embedded cholesterol in the nicotinic acetylcholine receptor. Proc. Natl. Acad. Sci. U.s.a.. 105:14418–14423.
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2019. Physics-based oligomeric models of the yeast mitofusin Fzo1 at the molecular scale in the context of membrane docking. Mitochondrion. 49:234–244.
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2019. Structural dataset from microsecond-long simulations of yeast mitofusin Fzo1 in the context of membrane docking.. Data Brief. 26:104460.
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2019. Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics. Scientific Reports. 9:16450.
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2021. Modeling Perturbations in Protein Filaments at the Micro and Meso Scale Using NAMD and PTools/Heligeom. Bio-protocol. 11:e4097.
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2015. An integrative approach to the study of filamentous oligomeric assemblies, with application to RecA. Plos One. in press:e0116414.
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2019. Weaving DNA strands: structural insight on ATP hydrolysis in RecA-induced homologous recombination. Nucleic Acids Res. 47:7798-7808.
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2022. Between Two Walls: Modeling the Adsorption Behavior of β-Glucosidase A on Bare and SAM-Functionalized Gold Surfaces.. Langmuir. 38(4):1313-1323.