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 …
[HTML][HTML] Understanding ligand-receptor non-covalent binding kinetics using molecular modeling
Z Tang, CC Roberts, AC Chia-en - Frontiers in bioscience …, 2017 - ncbi.nlm.nih.gov
Kinetic properties may serve as critical differentiators and predictors of drug efficacy and
safety, in addition to the traditionally focused binding affinity. However the quantitative …
safety, in addition to the traditionally focused binding affinity. However the quantitative …
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 …
[HTML][HTML] Enhanced-sampling simulations for the estimation of ligand binding kinetics: current status and perspective
The dissociation rate (k off) associated with ligand unbinding events from proteins is a
parameter of fundamental importance in drug design. Here we review recent major …
parameter of fundamental importance in drug design. Here we review recent major …
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 …
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 …
Prediction of the drug–target binding kinetics for flexible proteins by comparative binding energy analysis
A Nunes-Alves, F Ormersbach… - Journal of Chemical …, 2021 - ACS Publications
There is growing consensus that the optimization of the kinetic parameters for drug–protein
binding leads to improved drug efficacy. Therefore, computational methods have been …
binding leads to improved drug efficacy. Therefore, computational methods have been …
Baseline model for predicting protein–ligand unbinding kinetics through machine learning
N Amangeldiuly, D Karlov… - Journal of Chemical …, 2020 - ACS Publications
Derivation of structure–kinetics relationships can help rational design and development of
new small-molecule drug candidates with desired residence times. Efforts are now being …
new small-molecule drug candidates with desired residence times. Efforts are now being …
Public data set of protein–ligand dissociation kinetic constants for quantitative structure–kinetics relationship studies
H Liu, M Su, HX Lin, R Wang, Y Li - ACS omega, 2022 - ACS Publications
Protein–ligand binding affinity reflects the equilibrium thermodynamics of the protein–ligand
binding process. Binding/unbinding kinetics is the other side of the coin. Computational …
binding process. Binding/unbinding kinetics is the other side of the coin. Computational …
Recent progress in molecular simulation methods for drug binding kinetics
Highlights•Drug-target binding kinetics contribute to drug efficacy.•Many molecular dynamics
approaches to studying binding kinetics have been reported.•High quality datasets enable …
approaches to studying binding kinetics have been reported.•High quality datasets enable …