Publications
] .
2020. Scalable molecular dynamics on CPU and GPU architectures with NAMD. The Journal of Chemical Physics. 153
.
2020. Scruter les molécules en réalité virtuelle, pour quoi faire ? L'Actualité Chimique. (448):23–26.
.
2020. Stability of Aβ11-40 Trimers with Parallel and Antiparallel β-Sheet Organizations in a Membrane-Mimicking Environment by Replica Exchange Molecular Dynamics Simulation. The Journal of Physical Chemistry B.
.
2020. Structural transitions in the RNA 7SK 5' hairpin and their effect on HEXIM binding. Nucleic Acids Res. 48:373-389.
.
2020. Tau R3-R4 Domain Dimer of the Wild Type and Phosphorylated Ser356 Sequences. I. In Solution by Atomistic Simulations.. J Phys Chem B.
.
2020. Temperature Unmasks Allosteric Propensity in a Thermophilic Malate Dehydrogenase via Dewetting and Collapse. The Journal of Physical Chemistry B. 124:1001-1008.
.
2020. Visualizing biomolecular electrostatics in virtual reality with UnityMol-APBS.. Protein Sci. 29(1):237-246.
.
2020. Visualizing protein structures - tools and trends.. Biochem Soc Trans.
.
2020. Water dynamics at electrified graphene interfaces: a jump model perspective. Phys Chem Chem Phys.
.
2021. Building intuition for binding free energy calculations: Bound state definition, restraints, and symmetry. The Journal of Chemical Physics. 154:204101.
.
2021. Fast and Accurate Multidimensional Free Energy Integration.. J Chem Theory Comput. 17(11):6789-6798.
.
2021. Influences of ssDNA-RecA Filament Length on the Fidelity of Homologous Recombination. Journal of Molecular Biology. 433:167143.
.
2021. Mechanistic Insights on Heme-to-Heme Transmembrane Electron Transfer Within NADPH Oxydases From Atomistic Simulations.. Front Chem. 9:650651.
.
2021. Modeling Perturbations in Protein Filaments at the Micro and Meso Scale Using NAMD and PTools/Heligeom. Bio-protocol. 11:e4097.
.
2021. Moving pictures: Reassessing docking experiments with a dynamic view of protein interfaces.. Proteins.
.
2021. When Order Meets Disorder: Modeling and Function of the Protein Interface in Fuzzy Complexes. Biomolecules. 11:1529.
.
2022. Between Two Walls: Modeling the Adsorption Behavior of β-Glucosidase A on Bare and SAM-Functionalized Gold Surfaces.. Langmuir. 38(4):1313-1323.
.
2022. Building Biological Relevance Into Integrative Modelling of Macromolecular Assemblies. Frontiers in Molecular Biosciences. 9:826136.
.
2022. Consistent Picture of Phosphate–Divalent Cation Binding from Models with Implicit and Explicit Electronic Polarization. J. Phys. Chem. B. 126(22):4022-4034.
.
2022. Design – a new way to look at old molecules. Journal of Integrative Bioinformatics. 19:20220020.
.
2022. Enhanced Sampling Methods for Molecular Dynamics Simulations [Article v1.0]. Living Journal of Computational Molecular Science. 4:1583.
.
2022. Human Learning for Molecular Simulations: The Collective Variables Dashboard in VMD.. J Chem Theory Comput. 18(3):1945-1956.
.
2022. Modeling the Dynamics of Protein-Protein Interfaces, How and Why? Molecules. 27:1841.
.
2022. Multiscale Computational Study of the Conformation of the Full-Length Intrinsically Disordered Protein MeCP2.. J Chem Inf Model. 62(4):958-970.
.
2022. Open-channel structure of a pentameric ligand-gated ion channel reveals a mechanism of leaflet-specific phospholipid modulation. Nature Communications. 13