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 …
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 …
Combined free-energy calculation and machine learning methods for understanding ligand unbinding kinetics
The determination of drug residence times, which define the time an inhibitor is in complex
with its target, is a fundamental part of the drug discovery process. Synthesis and …
with its target, is a fundamental part of the drug discovery process. Synthesis and …
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 …
Estimation of kinetic and thermodynamic ligand-binding parameters using computational strategies
G Deganutti, S Moro - Future Medicinal Chemistry, 2017 - Future Science
Kinetic and thermodynamic ligand–protein binding parameters are gaining growing
importance as key information to consider in drug discovery. The determination of the …
importance as key information to consider in drug discovery. The determination of the …
A workflow for exploring ligand dissociation from a macromolecule: Efficient random acceleration molecular dynamics simulation and interaction fingerprint analysis of …
The dissociation of ligands from proteins and other biomacromolecules occurs over a wide
range of timescales. For most pharmaceutically relevant inhibitors, these timescales are far …
range of timescales. For most pharmaceutically relevant inhibitors, these timescales are far …
Kinetic rate constant prediction supports the conformational selection mechanism of protein binding
The prediction of protein-protein kinetic rate constants provides a fundamental test of our
understanding of molecular recognition, and will play an important role in the modeling of …
understanding of molecular recognition, and will play an important role in the modeling of …
Estimation of drug-target residence time by targeted molecular dynamics simulations
S Ziada, J Diharce, E Raimbaud… - Journal of Chemical …, 2022 - ACS Publications
Drug-target residence time has emerged as a key selection factor in drug discovery since
the binding duration of a drug molecule to its protein target can significantly impact its in vivo …
the binding duration of a drug molecule to its protein target can significantly impact its in vivo …
Qualitative estimation of protein–ligand complex stability through thermal titration molecular dynamics simulations
The prediction of ligand efficacy has long been linked to thermodynamic properties such as
the equilibrium dissociation constant, which considers both the association and the …
the equilibrium dissociation constant, which considers both the association and the …
Computationally predicting binding affinity in protein–ligand complexes: free energy-based simulations and machine learning-based scoring functions
Accurately predicting protein–ligand binding affinities can substantially facilitate the drug
discovery process, but it remains as a difficult problem. To tackle the challenge, many …
discovery process, but it remains as a difficult problem. To tackle the challenge, many …