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 …

[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 …

[HTML][HTML] Rapid quantification of protein-ligand binding via 19F NMR lineshape analysis

SS Stadmiller, JS Aguilar, CA Waudby, GJ Pielak - Biophysical journal, 2020 - cell.com
Fluorine incorporation is ideally suited to many NMR techniques, and incorporation of
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

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 …

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 …

Ligand unbinding pathway and mechanism analysis assisted by machine learning and graph methods

S Bray, V Tänzel, S Wolf - Journal of Chemical Information and …, 2022 - ACS Publications
We present two methods to reveal protein–ligand unbinding mechanisms in biased
unbinding simulations by clustering trajectories into ensembles representing unbinding …

KBbox: A toolbox of computational methods for studying the kinetics of molecular binding

NJ Bruce, GK Ganotra, S Richter… - Journal of chemical …, 2019 - ACS Publications
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 …

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 …

[HTML][HTML] In silico prediction of siRNA ionizable-lipid nanoparticles In vivo efficacy: Machine learning modeling based on formulation and molecular descriptors

AA Metwally, AA Nayel, RM Hathout - Frontiers in Molecular …, 2022 - frontiersin.org
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 …

[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 …