Recent Advancements in Computing Reliable Binding Free Energies in Drug Discovery Projects

NA Murugan, V Poongavanam… - … : Applications in Preclinical …, 2019 - Springer
In recent times, our healthcare system is being challenged by many drug-resistant
microorganisms and ageing-associated diseases for which we do not have any drugs or …

The slow but steady rise of binding free energy calculations in drug discovery

H Xu - Journal of Computer-Aided Molecular Design, 2023 - Springer
Binding free energy calculations are increasingly used in drug discovery research to predict
protein-ligand binding affinities and to prioritize candidate drug molecules accordingly. It has …

Large scale study of ligand–protein relative binding free energy calculations: actionable predictions from statistically robust protocols

AP Bhati, PV Coveney - Journal of Chemical Theory and …, 2022 - ACS Publications
The accurate and reliable prediction of protein–ligand binding affinities can play a central
role in the drug discovery process as well as in personalized medicine. Of considerable …

Fast, routine free energy of binding estimation using MovableType

LM Westerhoff, Z Zheng - Free Energy Methods in Drug Discovery …, 2021 - ACS Publications
Rigorous free energy of binding estimation using biomolecular structural ensembles has
been of significant interest to the computational chemistry field for decades. With the advent …

Prediction of protein–ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations

J Michel, JW Essex - Journal of computer-aided molecular design, 2010 - Springer
Many limitations of current computer-aided drug design arise from the difficulty of reliably
predicting the binding affinity of a small molecule to a biological target. There is thus a strong …

[PDF][PDF] Automating Free Energy Perturbation Calculations For Drug Design

SN Zavitsanou - Department of Informatics and …, 2018 - pergamos.lib.uoa.gr
The advent of technological advances of computer-aided drug design has streamlined the
drug design process, rendering it more cost-and time-efficient. Nowadays, rational structure …

Recent advances in alchemical binding free energy calculations for drug discovery

I Muegge, Y Hu - ACS Medicinal Chemistry Letters, 2023 - ACS Publications
Rigorous physics-based methods to calculate binding free energies of protein–ligand
complexes have become a valued component of structure-based drug design. Relative and …

Free energy methods in drug design: prospects of “alchemical perturbation” in medicinal chemistry: miniperspective

BJ Williams-Noonan, E Yuriev… - Journal of medicinal …, 2018 - ACS Publications
Underpinning all drug discovery projects is the interaction between a drug and its target,
usually a protein. Thus, improved methods for predicting the magnitude of protein–ligand …

Automation of absolute protein-ligand binding free energy calculations for docking refinement and compound evaluation

G Heinzelmann, MK Gilson - Scientific reports, 2021 - nature.com
Absolute binding free energy calculations with explicit solvent molecular simulations can
provide estimates of protein-ligand affinities, and thus reduce the time and costs needed to …

Free energy calculations: use and limitations in predicting ligand binding affinities

MR Reddy, MD Erion, A Agarwal - Reviews in computational …, 2000 - Wiley Online Library
In the early 1980s, advances in protein crystallography and substantial gains in computer
power suggested that drug discovery research was on the verge of a new age, l an age in …