Proteins and DNA
Proteins and DNA
Selected Publications (2001- )
Reduced point charge models of proteins: Assessment based on molecular dynamics simulations, Leherte, L. Molecular Simulation. 42 (2016) 289-304
Multiscale design of coarse-grained elastic network-based potentials for the μ opioid receptor, Fossépré, M., Leherte, L., Laaksonen, A. & Vercauteren, D.P. Journal of Molecular Modeling. 22 (2016) 227
Systematic hierarchical coarse-graining with the inverse Monte Carlo method, Lyubartsev, A.P., Naome, A., Vercauteren, D.P., Laaksonen. The journal of chemical physics 143 (2015) 243120
A Coarse-Grained Simulation Study of the Structures, Energetics, and Dynamics of Linear and Circular DNA with Its Ions, Naome, A., Laaksonen, A. & Vercauteren, D.P. Journal of Chemical Theory and Computation 11 (2015) 2813-2826
A solvent-mediated coarse-grained model of DNA derived with the systematic Newton inversion method, Naômé A., Laaksonen A. & Vercauteren D.P. Journal of Chemical Theory and Computation 10 (2014) 3541-3549
On the modularity of the intrinsic flexibility of the μ opioid receptor: A computational study, Fossépré M., Leherte L., Laaksonen A. & Vercauteren D.P. PLoS ONE 9 (2014) 29 p.e115856
Comparison of reduced point charge models of proteins: Molecular dynamics simulations of Ubiquitin, Leherte L. & Vercauteren D.P., SCIENCE CHINA Chemistry 57 (2014) 1340-1354
Implementation of a protein reduced point charge model toward molecular dynamics applications, Leherte L. & Vercauteren D.P. Journal of Physical Chemistry A 115 (2011) 12531-12543
Charge density distributions derived from smoothed electrostatic potential functions: Design of protein reduced point charge models, Leherte L. & Vercauteren D.P. Journal of Computer-Aided Molecular Design 25 (2011) 913-930
Molecular dynamics simulation of 8-oxoguanine containing DNA fragments reveals altered hydration and ion binding patterns, Naômé A., Vercauteren D.P., Schyman P. & Laaksonen A. Journal of Physical Chemistry B 114 (2010) 4789-4801
Coarse point charge models for proteins from smoothed molecular electrostatic potentials, Leherte L. & Vercauteren D.P. Journal of Chemical Theory and Computation 5 (2009) 3279-3298
Collective motions of rigid fragments in protein structures from smoothed electron density distributions, Leherte L. & Vercauteren D.P. Journal of Computational Chemistry 29 (2008) 1472-1489
Topological analysis of proteins as derived from medium and high resolution electron density: Applications to electrostatic properties, Leherte, L., Guillot, B., Vercauteren, D.P., Pichon-Pesme, V., Jelsch, C., Lagoutte, A. & Lecomte, C. 2007 The Quantum Theory of Atoms in Molecules - From Solid State to DNA and Drug Design. Matta C.F. & Boyd R.J. (eds.). Weinheim, Germany: Wiley-VCH, p. 285-316
Hierarchical analysis of promolecular full electron-density distributions: Description of protein structure fragments, Leherte L. Acta Crystallographica Section D 60 (2004) 1254-1265
PhD Theses
R. Cosquer, Theoretical study of opioid receptor self-assembly by hybrid methods to elaborate bitopic ligands (in progress) Cosquer R.
Effet de la composition lipidique de la membrane plasmique sur les propriétés du récepteur opioïde µ par dynamique moléculaire multi-échelle (en cours) Angladon M.-A.
Large scale simulations of DNA-containing systems (in progress) Naômé A.
Development of a limited side-effect anesthetic and studies of the µ opioid and NR2B receptors dynamics by stastistical mechanics simulations based on a multi-scale force field (2015) Fossépré M.
Étude de la formation et des propriétés dynamiques, conformationelles et énergétiques d'assemblages supramoléculaires à base de nanotubes organiques et d'agrégats d'argent dans des brins d'ADN (2014) Staelens N.
Master Theses
Prédiction par des méthodes théoriques de la structure 3D du récepteur opioïde μ pour la conception d’un anesthésiant à effets secondaires limités (2010) Fossépré M.
Theoretical study of healthy and damaged DNA fragments in solution using Molecular Dynamics simulations (2009) Naômé A.
Classification de points critiques de cartes de densité électronique de protéines à moyenne résolution (2000) Binamé J.
Study of the CD2/CD58 protein-protein interface with the perspective to elaborate new ligands (in progress) Petit A.
