Relative binding free energy calculations with transformato: A molecular dynamics engine-independent tool.

ABSTRACT: We present the software package transformato for the setup of large-scale relative binding free energy calculations. Transformato is written in Python as an open source project (https://github.com/wiederm/transformato); in contrast to comparable tools, it is not closely tied to a particular molecular dynamics engine to carry out the underlying simulations. Instead of alchemically transforming a ligand L ₁ directly into another L ₂, the two ligands are mutated to a common core. Thus, while dummy atoms are required at intermediate states, in particular at the common core state, none are present at the physical endstates. To validate the method, we calculated 76 relative binding free energy differences Δ Δ G L 1 → L 2 b i n d for five protein-ligand s

SUBMITTER: Karwounopoulos J 

PROVIDER: S-EPMC9485484 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature