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 …
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 …
Kinetics of ligand–protein dissociation from all-atom simulations: Are we there yet?
Large parallel gains in the development of both computational resources and sampling
methods have now made it possible to simulate dissociation events in ligand–protein …
methods have now made it possible to simulate dissociation events in ligand–protein …
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 …
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 …
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 …
Can one trust kinetic and thermodynamic observables from biased metadynamics simulations?: Detailed quantitative benchmarks on millimolar drug fragment …
D Pramanik, Z Smith, A Kells… - The Journal of Physical …, 2019 - ACS Publications
Understanding ligand dissociation mechanisms at an atomic resolution is a highly desired
but difficult to achieve objective in experiments as well as in computer simulations. Structural …
but difficult to achieve objective in experiments as well as in computer simulations. Structural …
Data-driven classification of ligand unbinding pathways
D Ray, M Parrinello - … of the National Academy of Sciences, 2024 - National Acad Sciences
Studying the pathways of ligand–receptor binding is essential to understand the mechanism
of target recognition by small molecules. The binding free energy and kinetics of protein …
of target recognition by small molecules. The binding free energy and kinetics of protein …
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 …
[HTML][HTML] Ligand unbinding mechanisms and kinetics for T4 lysozyme mutants from τRAMD simulations
The protein-ligand residence time, τ, influences molecular function in biological networks
and has been recognized as an important determinant of drug efficacy. To predict τ …
and has been recognized as an important determinant of drug efficacy. To predict τ …