Research Topic
molecular dynamics
11 publications exploring this topic
2024
In silico screening of LRRK2 WDR domain inhibitors using deep docking and free energy simulations
(2024)
The Critical Assessment of Computational Hit-Finding Experiments (CACHE) Challenge series is focused on identifying small molecule inhibitors of protein targets using computational methods.
2023
In silico screening of LRRK2 WDR domain inhibitors using deep docking and free energy simulations
(2023)
The Critical Assessment of Computational Hit-Finding Experiments (CACHE) Challenge is focused on identifying small molecule inhibitors of protein targets using computational methods.
Exploring the frontiers of condensed-phase chemistry with a general reactive machine learning potential
(2023)
Abstract Reactive chemistry atomistic simulation has a broad range of applications from drug design to energy to materials discovery.
2022
Active learning guided drug design lead optimization based on relative binding free energy modeling
(2022)
In silico identification of potent protein inhibitors commonly requires prediction of a ligand binding free energy (BFE).
2012
In silico structure–function analysis of E. cloacae nitroreductase
Proteins: Structure, Function, and Bioinformatics, 80, 2728–2741 (2012)
AbstractReduction, catalyzed by the bacterial nitroreductases, is the quintessential first step in the biodegradation of a variety of nitroaromatic compounds from contaminated waters and soil.
2011
Car–Parrinello Molecular Dynamics Simulations of Tensile Tests on Si⟨001⟩ Nanowires
The Journal of Physical Chemistry C, 115, 12283–12292 (2011)
Car–Parrinello Molecular Dynamics Simulations of Tensile Tests on Si⟨001⟩ Nanowires.
2010
Hydration of nucleic acid bases: a Car–Parrinello molecular dynamics approach
Physical Chemistry Chemical Physics, 12, 3363 (2010)
Hydration of nucleic acid bases: a Car–Parrinello molecular dynamics approach.
New insight on structural properties of hydrated nucleic acid bases from ab initio molecular dynamics
Physical Chemistry Chemical Physics, 12, 9945 (2010)
New insight on structural properties of hydrated nucleic acid bases from ab initio molecular dynamics.
2008
Ab Initio Molecular Dynamics Study on the Initial Chemical Events in Nitramines: Thermal Decomposition of CL-20
The Journal of Physical Chemistry B, 112, 11005–11013 (2008)
Ab Initio Molecular Dynamics Study on the Initial Chemical Events in Nitramines: Thermal Decomposition of CL-20.
2007
Are Isolated Nucleic Acid Bases Really Planar? A Car−Parrinello Molecular Dynamics Study
The Journal of Physical Chemistry B, 111, 3476–3480 (2007)
Are Isolated Nucleic Acid Bases Really Planar? A Car−Parrinello Molecular Dynamics Study.
Theoretical calculations: Can Gibbs free energy for intermolecular complexes be predicted efficiently and accurately?
Journal of Computational Chemistry, 28, 1598–1609 (2007)
AbstractThe theoretical study has been performed to refine the procedure for calculations of Gibbs free energy with a relative accuracy of less than 1 kcal/mol.