Predicting protein–ligand binding and unbinding kinetics with biased MD simulations and coarse-graining of dynamics: Current state and challenges
S Wolf - Journal of Chemical Information and Modeling, 2023 - ACS Publications
The prediction of drug–target binding and unbinding kinetics that occur on time scales
between milliseconds and several hours is a prime challenge for biased molecular …
between milliseconds and several hours is a prime challenge for biased molecular …
A supervised molecular dynamics approach to unbiased ligand–protein unbinding
The recent paradigm shift toward the use of the kinetics parameters in place of
thermodynamic constants is leading the computational chemistry community to develop …
thermodynamic constants is leading the computational chemistry community to develop …
Kinetics of ligand binding through advanced computational approaches: a review
Ligand residence times and binding rates have been found to be useful quantities to
consider during drug design. The underlying structural and dynamic determinants of these …
consider during drug design. The underlying structural and dynamic determinants of these …
Thermodynamics and kinetics of drug-target binding by molecular simulation
S Decherchi, A Cavalli - Chemical Reviews, 2020 - ACS Publications
Computational studies play an increasingly important role in chemistry and biophysics,
mainly thanks to improvements in hardware and algorithms. In drug discovery and …
mainly thanks to improvements in hardware and algorithms. In drug discovery and …
Perspectives on Ligand/Protein Binding Kinetics Simulations: Force Fields, Machine Learning, Sampling, and User-Friendliness
Computational techniques applied to drug discovery have gained considerable popularity
for their ability to filter potentially active drugs from inactive ones, reducing the time scale …
for their ability to filter potentially active drugs from inactive ones, reducing the time scale …
Toward high-throughput predictive modeling of protein binding/unbinding kinetics
SH Chiu, L Xie - Journal of chemical information and modeling, 2016 - ACS Publications
One of the unaddressed challenges in drug discovery is that drug potency determined in
vitro is not a reliable indicator of drug activity in vivo. Accumulated evidence suggests that in …
vitro is not a reliable indicator of drug activity in vivo. Accumulated evidence suggests that in …
Predicting biomolecular binding kinetics: A review
Biomolecular binding kinetics including the association (k on) and dissociation (k off) rates
are critical parameters for therapeutic design of small-molecule drugs, peptides, and …
are critical parameters for therapeutic design of small-molecule drugs, peptides, and …
Molecular dynamics simulations and kinetic measurements to estimate and predict protein–ligand residence times
L Mollica, I Theret, M Antoine… - Journal of medicinal …, 2016 - ACS Publications
Ligand–target residence time is emerging as a key drug discovery parameter because it can
reliably predict drug efficacy in vivo. Experimental approaches to binding and unbinding …
reliably predict drug efficacy in vivo. Experimental approaches to binding and unbinding …
Roles of Accelerated Molecular Dynamics Simulations in Predictions of Binding Kinetic Parameters
J Chen, W Wang, H Sun, W He - Mini Reviews in Medicinal …, 2024 - ingentaconnect.com
Rational predictions on binding kinetics parameters of drugs to targets play significant roles
in future drug designs. Full conformational samplings of targets are requisite for accurate …
in future drug designs. Full conformational samplings of targets are requisite for accurate …
Investigating drug–target residence time in kinases through enhanced sampling simulations
D Gobbo, V Piretti, RMC Di Martino… - Journal of Chemical …, 2019 - ACS Publications
It is widely accepted that drug–target association and dissociation rates directly affect drug
efficacy and safety. To rationally optimize drug binding kinetics, one must know the atomic …
efficacy and safety. To rationally optimize drug binding kinetics, one must know the atomic …