Molecular dynamics-driven drug discovery: leaping forward with confidence
Highlights•Currently, developing a market-approved drug costs a staggering $2.6 billion.•In
silico methods have become an important strategy for narrowing down on promising lead …
silico methods have become an important strategy for narrowing down on promising lead …
On the inner workings of Monte Carlo codes
D Dubbeldam, A Torres-Knoop, KS Walton - Molecular Simulation, 2013 - Taylor & Francis
We review state-of-the-art Monte Carlo (MC) techniques for computing fluid coexistence
properties (Gibbs simulations) and adsorption simulations in nanoporous materials such as …
properties (Gibbs simulations) and adsorption simulations in nanoporous materials such as …
Direct calculation of liquid–vapor phase equilibria from transition matrix Monte Carlo simulation
JR Errington - The Journal of chemical physics, 2003 - pubs.aip.org
An approach for directly determining the liquid–vapor phase equilibrium of a model system
at any temperature along the coexistence line is described. The method relies on transition …
at any temperature along the coexistence line is described. The method relies on transition …
Modelling and enhanced molecular dynamics to steer structure-based drug discovery
S Kalyaanamoorthy, YPP Chen - Progress in biophysics and molecular …, 2014 - Elsevier
The ever-increasing gap between the availabilities of the genome sequences and the crystal
structures of proteins remains one of the significant challenges to the modern drug discovery …
structures of proteins remains one of the significant challenges to the modern drug discovery …
The ice/water interface: Molecular dynamics simulations of the basal, prism,{2021}, and {2110} interfaces of ice Ih
JA Hayward, ADJ Haymet - The Journal of Chemical Physics, 2001 - pubs.aip.org
The structure and dynamics of the 0001 basal, 101 0 prism, 202 1, and 21 1 0 ice Ih/water
interfaces have been investigated using molecular dynamics and the flexible CF1 central …
interfaces have been investigated using molecular dynamics and the flexible CF1 central …
[HTML][HTML] Quantifying free energies through local composition fluctuations in binary solid solutions: A proof-of-concept study using atomistic embedded-atom …
D Bitter, M Poul, G Schmitz, SM Eich - Acta Materialia, 2024 - Elsevier
While thermodynamic fluctuation theory has been extensively utilized in liquids for decades
to obtain direct thermodynamic information, such as Gibbs free energies, from local …
to obtain direct thermodynamic information, such as Gibbs free energies, from local …
A molecular theory of the homogeneous nucleation rate. I. Formulation and fundamental issues
A molecular theory of the rate of homogeneous vapor phase nucleation is formulated. The
ultimate goal is a theory that contains no ad hoc assumptions or arbitrary parameters having …
ultimate goal is a theory that contains no ad hoc assumptions or arbitrary parameters having …
[HTML][HTML] Novel barostat implementation for molecular dynamics
J Janek, J Kolafa - The Journal of Chemical Physics, 2024 - pubs.aip.org
We propose a novel implementation of the extended-dynamics equations for isothermal–
isobaric ensemble in molecular dynamics, as the Martyna–Tobias–Klein thermostat and …
isobaric ensemble in molecular dynamics, as the Martyna–Tobias–Klein thermostat and …
Systematic formulation of thermodynamic properties in the ensemble
P Ströker, R Hellmann, K Meier - Physical Review E, 2021 - APS
Molecular expressions for thermodynamic properties and derivatives of the Gibbs energy up
to third order in the isobaric-isothermal (N p T) ensemble are systematically derived using …
to third order in the isobaric-isothermal (N p T) ensemble are systematically derived using …