Advances in computational methods for ligand binding kinetics

F Sohraby, A Nunes-Alves - Trends in Biochemical Sciences, 2023 - cell.com
Binding kinetic parameters can be correlated with drug efficacy, which in recent years led to
the development of various computational methods for predicting binding kinetic rates and …

RNA–ligand molecular docking: Advances and challenges

Y Zhou, Y Jiang, SJ Chen - Wiley Interdisciplinary Reviews …, 2022 - Wiley Online Library
With rapid advances in computer algorithms and hardware, fast and accurate virtual
screening has led to a drastic acceleration in selecting potent small molecules as drug …

The importance of binding kinetics and drug–target residence time in pharmacology

KE Knockenhauer, RA Copeland - British Journal of …, 2024 - Wiley Online Library
A dominant assumption in pharmacology throughout the 20th century has been that in vivo
target occupancy—and attendant pharmacodynamics—depends on the systemic …

Predicting biomolecular binding kinetics: A review

J Wang, HN Do, K Koirala, Y Miao - Journal of Chemical Theory …, 2023 - ACS Publications
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 …

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 …

Transition rates and efficiency of collective variables from time-dependent biased simulations

K Palacio-Rodriguez, H Vroylandt… - The journal of …, 2022 - ACS Publications
Simulations with adaptive time-dependent bias enable an efficient exploration of the
conformational space of a system. However, the dynamic information is altered by the bias …