Modern alchemical free energy methods for drug discovery explained
DM York - ACS Physical Chemistry Au, 2023 - ACS Publications
This Perspective provides a contextual explanation of the current state-of-the-art alchemical
free energy methods and their role in drug discovery as well as highlights select emerging …
free energy methods and their role in drug discovery as well as highlights select emerging …
An overview of the SAMPL8 host–guest binding challenge
The SAMPL series of challenges aim to focus the community on specific modeling
challenges, while testing and hopefully driving progress of computational methods to help …
challenges, while testing and hopefully driving progress of computational methods to help …
Performance and Analysis of the Alchemical Transfer Method for Binding-Free-Energy Predictions of Diverse Ligands
The Alchemical Transfer Method (ATM) is herein validated against the relative binding-free
energies (RBFEs) of a diverse set of protein–ligand complexes. We employed a streamlined …
energies (RBFEs) of a diverse set of protein–ligand complexes. We employed a streamlined …
Alchemical Enhanced Sampling with Optimized Phase Space Overlap
An alchemical enhanced sampling (ACES) method has recently been introduced to facilitate
importance sampling in free energy simulations. The method achieves enhanced sampling …
importance sampling in free energy simulations. The method achieves enhanced sampling …
Taming multiple binding poses in alchemical binding free energy prediction: the β-cyclodextrin host–guest SAMPL9 blinded challenge
We apply the Alchemical Transfer Method (ATM) and a bespoke fixed partial charge force
field to the SAMPL9 bCD host–guest binding free energy prediction challenge that …
field to the SAMPL9 bCD host–guest binding free energy prediction challenge that …
The SAMPL9 host-guest blind challenge: an overview of binding free energy predictive accuracy
We report the results of the SAMPL9 host–guest blind challenge for predicting binding free
energies. The challenge focused on macrocycles from pillar [n]-arene and cyclodextrin host …
energies. The challenge focused on macrocycles from pillar [n]-arene and cyclodextrin host …
Developing end-point methods for absolute binding free energy calculation using the Boltzmann-quasiharmonic model
Understanding the physical forces underlying receptor–ligand binding requires robust
methods for analyzing the binding thermodynamics. In end-point binding free energy …
methods for analyzing the binding thermodynamics. In end-point binding free energy …
Expanded ensemble predictions of absolute binding free energies in the SAMPL9 host–guest challenge
MFD Hurley, RM Raddi, JG Pattis… - Physical Chemistry …, 2023 - pubs.rsc.org
As part of the SAMPL9 community-wide blind host–guest challenge, we implemented an
expanded ensemble workflow to predict absolute binding free energies for 13 small …
expanded ensemble workflow to predict absolute binding free energies for 13 small …
Binding Selectivity Analysis from Alchemical Receptor Hopping and Ligand Swapping Free Energy Calculations
S Azimi, E Gallicchio - arXiv preprint arXiv:2402.06887, 2024 - arxiv.org
We present receptor-hopping and ligand-swapping free energy estimation protocols based
on the Alchemical Transfer Method (ATM) to model the binding selectivity of a set of ligands …
on the Alchemical Transfer Method (ATM) to model the binding selectivity of a set of ligands …
Potential Distribution Theory of Alchemical Transfer
S Azimi, E Gallicchio - arXiv preprint arXiv:2407.14713, 2024 - arxiv.org
We present an analytical description of the Alchemical Transfer Method (ATM) for molecular
binding using the Potential Distribution Theory (PDT) formalism. ATM models the binding …
binding using the Potential Distribution Theory (PDT) formalism. ATM models the binding …