Perspectives on Ligand/Protein Binding Kinetics Simulations: Force Fields, Machine Learning, Sampling, and User-Friendliness

P Conflitti, S Raniolo, V Limongelli - Journal of Chemical Theory …, 2023 - ACS Publications
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 …

Recent progress in molecular simulation methods for drug binding kinetics

A Nunes-Alves, DB Kokh, RC Wade - Current Opinion in Structural Biology, 2020 - Elsevier
Highlights•Drug-target binding kinetics contribute to drug efficacy.•Many molecular dynamics
approaches to studying binding kinetics have been reported.•High quality datasets enable …

Understanding the impact of binding free energy and kinetics calculations in modern drug discovery

VA Adediwura, K Koirala, HN Do, J Wang… - Expert Opinion on Drug …, 2024 - Taylor & Francis
Introduction For rational drug design, it is crucial to understand the receptor-drug binding
processes and mechanisms. A new era for the use of computer simulations in predicting …

Kinetics of ligand binding through advanced computational approaches: a review

A Dickson, P Tiwary, H Vashisth - Current topics in medicinal …, 2017 - ingentaconnect.com
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 …

[HTML][HTML] Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations

L Mollica, S Decherchi, SR Zia, R Gaspari, A Cavalli… - Scientific reports, 2015 - nature.com
Drug discovery is expensive and high-risk. Its main reasons of failure are lack of efficacy and
toxicity of a drug candidate. Binding affinity for the biological target has been usually …

[HTML][HTML] A molecular-modeling toolbox aimed at bridging the gap between medicinal chemistry and computational sciences

S Eid, A Zalewski, M Smieško, B Ernst… - International journal of …, 2013 - mdpi.com
In the current era of high-throughput drug discovery and development, molecular modeling
has become an indispensable tool for identifying, optimizing and prioritizing small-molecule …

[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 …

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 …

15 Years of molecular simulation of drug-binding kinetics

CF Wong - Expert Opinion on Drug Discovery, 2023 - Taylor & Francis
Introduction Drug-binding kinetics has been increasingly recognized as an important factor
to be considered in drug discovery. Long residence time could prolong the action of some …

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 …