ACES: optimized alchemically enhanced sampling
We present an alchemical enhanced sampling (ACES) method implemented in the GPU-
accelerated AMBER free energy MD engine. The methods hinges on the creation of an …
accelerated AMBER free energy MD engine. The methods hinges on the creation of an …
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 …
De novo design of drug-binding proteins with predictable binding energy and specificity
The de novo design of small molecule–binding proteins has seen exciting recent progress;
however, high-affinity binding and tunable specificity typically require laborious screening …
however, high-affinity binding and tunable specificity typically require laborious screening …
Relative binding free energy calculations for ligands with diverse scaffolds with the alchemical transfer method
We present an extension of the alchemical transfer method (ATM) for the estimation of
relative binding free energies of molecular complexes applicable to conventional, as well as …
relative binding free energies of molecular complexes applicable to conventional, as well as …
What to Make of Zero: Resolving the Statistical Noise from Conformational Reorganization in Alchemical Binding Free Energy Estimates with Metadynamics Sampling
S Khuttan, E Gallicchio - Journal of Chemical Theory and …, 2024 - ACS Publications
We introduce the self-relative binding free energy (self-RBFE) approach to evaluate the
intrinsic statistical variance of dual-topology alchemical binding free energy estimators. The …
intrinsic statistical variance of dual-topology alchemical binding free energy estimators. The …
PyAutoFEP: An automated free energy perturbation workflow for GROMACS integrating enhanced sampling methods
L Carvalho Martins, EA Cino… - Journal of Chemical …, 2021 - ACS Publications
Free energy perturbation (FEP) calculations are now routinely used in drug discovery to
estimate the relative FEB (RFEB) of small molecules to a biomolecular target of interest …
estimate the relative FEB (RFEB) of small molecules to a biomolecular target of interest …
Alchemical transfer approach to absolute binding free energy estimation
The alchemical transfer method (ATM) for the calculation of standard binding free energies
of noncovalent molecular complexes is presented. The method is based on a coordinate …
of noncovalent molecular complexes is presented. The method is based on a coordinate …
Validation of the Alchemical Transfer Method for the Estimation of Relative Binding Affinities of Molecular Series
F Sabanés Zariquiey, A Pérez… - Journal of chemical …, 2023 - ACS Publications
The accurate prediction of protein–ligand binding affinities is crucial for drug discovery.
Alchemical free energy calculations have become a popular tool for this purpose. However …
Alchemical free energy calculations have become a popular tool for this purpose. However …
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 …
Recent advances in solvation modeling applications: Chemical properties, reaction mechanisms and catalysis
In this work, we review recent studies in the field of computational solvation. Methods at
different scales from ab initio to force field calculations with both implicit solvent and explicit …
different scales from ab initio to force field calculations with both implicit solvent and explicit …