ABFE_workflow: Automated Absolute Binding Free Energy Calculation Workflow for Drug Discovery
Benchmarks
Merck FEP Benchmark: Benchmark set for relative free energy calculations.
OpenFF Benchmark: Protein-Ligand Benchmark Dataset for testing Parameters and Methods of Free Energy Calculations.
Classical
alchemlyb:
BAT2:
BAT: Binding Affinity Tool (BAT.py) is a python tool for fully automated absolute binding free energy (ABFE) calculations using all-atom Molecular Dynamics (MD)
FEgrow: An interactive workflow for building user-defined congeneric series of ligands in protein binding pockets for input to free energy calculations.
gufe: GUFE is a toolkit for developers of software related to alchemical free energy calculations, containing data models and abstract base classes.
OpenFE: A Python package for executing alchemical free energy calculations
pAPRika: pAPRika is a toolkit for setting up, running, and analyzing free energy molecular dynamics simulations.
Guides
Best Practices for Alchemical Free Energy Simulations:
ML-enabled
ATM_with_NNPs: Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials
Planning
HiMap: High Information Mapper (HiMap), successor of the Lead Optimization Mapper (LOMAP), includes design generation based on statistical optimality for alchemical free energy calculations and optimization of free energy perturbation networks.
Thermodynamics Ensemble
DynaFormer: deep learning model to predict the binding affinities based on dynamic protein-ligand interactions
Tools
Kartograf: Kartograf is a package focusing on 3D geometry-based atom mappings, useful for generating hybrid topology systems in free energy calculations and other applications. .)
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