Development of methods in computational structural biology
We are developing new computational methods to calculate the electrostatics of proteins, understand their dynamical properties and simulate transitions between two known conformations of the same macromolecule.
DNA Polymerases Engineering and Synthetic Biology
We work with archaeal DNA polymerases (PolB) that were evolved to accept xeno-nucleotides to understand the molecular basis of their changed specificity. We use this information to engineer new DNA polymerases to synthesize variants […]
DNA Repair and Cancer
We study the mechanism of DNA Repair of (DNA) Double Strand Breaks through the so-called Non-Homologous End Joining (NHEJ) process in mammals using x-ray crystallography and structural studies of pol mu and Tdt
Ligand-gated Ion channels
We study the structure and function of ligand-gated ion channels by X-ray crystallography to understand i) the gating mechanism (opening of the pore upon agonist binding) ii) the permeation mechanism (transport of ions through […]
This software allows to calculate the most probable pathway between two conformational states of the same macromolecule, using the Elastic Network model for the Energy landscape of each of the two states. See http://lorentz.dynstr.pasteur.fr/joel/index.php
We have developed a new way to calculate electrostatics properties of biological macromolecules in a polarizable solvent: AquaSol. We can then compute the solvent density around proteins as well as their SAXS spectra: AquaSAXS.
2021Parameterizing elastic network models to capture the dynamics of proteins., J Comput Chem. 2021 Jun 11..
2021Physics approach to the variable-mass optimal-transport problem, Phys Rev E . 2021 Jan;103(1-1):012113..
2021Simultaneous Identification of Multiple Binding Sites in Proteins: A Statistical Mechanics Approach., J Phys Chem B. 2021 May 20;125(19):5052-5067..
2021Fast and efficient purification of SARS-CoV-2 RNA dependent RNA polymerase complex expressed in Escherichia coli., PLoS One. 2021 Apr 29;16(4):e0250610.
2021How cyanophage S-2L rejects adenine and incorporates 2-aminoadenine to saturate hydrogen bonding in its DNA., Nat Commun 2021 04; 12(1): 2420.
2020Structural Studies of HNA Substrate Specificity in Mutants of an Archaeal DNA Polymerase Obtained by Directed Evolution, Biomolecules . 2020 Dec 8;10(12):1647. doi: 10.3390/biom10121647..
2020Structural evidence for the binding of monocarboxylates and dicarboxylates at pharmacologically relevant extracellular sites of a pentameric ligand-gated ion channel., Acta Crystallogr D Struct Biol 2020 Jul; 76(Pt 7): 668-675.
2020Structural basis for allosteric transitions of a multidomain pentameric ligand-gated ion channel., Proc. Natl. Acad. Sci. U.S.A. 2020 Jun; 117(24): 13437-13446.
2020Structural basis for the increased processivity of D-family DNA polymerases in complex with PCNA., Nat Commun 2020 03; 11(1): 1591.
2019Statistical Physics Approach to the Optimal Transport Problem., Phys. Rev. Lett. 2019 Jul; 123(4): 040603.
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