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] Therapeutic drug repositioning with special emphasis on neurodegenerative diseases: Threats and issues
BB Kakoti, R Bezbaruah, N Ahmed - Frontiers in Pharmacology, 2022 - frontiersin.org
Drug repositioning or repurposing is the process of discovering leading-edge indications for
authorized or declined/abandoned molecules for use in different diseases. This approach …
authorized or declined/abandoned molecules for use in different diseases. This approach …
[HTML][HTML] Rapid quantification of protein-ligand binding via 19F NMR lineshape analysis
Fluorine incorporation is ideally suited to many NMR techniques, and incorporation of
fluorine into proteins and fragment libraries for drug discovery has become increasingly …
fluorine into proteins and fragment libraries for drug discovery has become increasingly …
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 …
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 …
Ligand unbinding pathway and mechanism analysis assisted by machine learning and graph methods
We present two methods to reveal protein–ligand unbinding mechanisms in biased
unbinding simulations by clustering trajectories into ensembles representing unbinding …
unbinding simulations by clustering trajectories into ensembles representing unbinding …
KBbox: A toolbox of computational methods for studying the kinetics of molecular binding
The past few years have seen increasing recognition of the importance of understanding
molecular binding kinetics. This has led to the development of myriad computational …
molecular binding kinetics. This has led to the development of myriad computational …
Applications of machine learning in computer-aided drug discovery
SMBA Turzo, ER Hantz, S Lindert - QRB discovery, 2022 - cambridge.org
Machine learning (ML) has revolutionised the field of structure-based drug design (SBDD) in
recent years. During the training stage, ML techniques typically analyse large amounts of …
recent years. During the training stage, ML techniques typically analyse large amounts of …
[HTML][HTML] In silico prediction of siRNA ionizable-lipid nanoparticles In vivo efficacy: Machine learning modeling based on formulation and molecular descriptors
In silico prediction of the in vivo efficacy of siRNA ionizable-lipid nanoparticles is desirable
as it can save time and resources dedicated to wet-lab experimentation. This study aims to …
as it can save time and resources dedicated to wet-lab experimentation. This study aims to …
[HTML][HTML] In silico prediction of the dissociation rate constants of small chemical ligands by 3D-grid-based VolSurf method
S Huang, L Chen, H Mei, D Zhang, T Shi… - International Journal of …, 2020 - mdpi.com
Accumulated evidence suggests that binding kinetic properties—especially dissociation rate
constant or drug-target residence time—are crucial factors affecting drug potency. However …
constant or drug-target residence time—are crucial factors affecting drug potency. However …