Free Energy Calculations

• 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:
  
• 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)
  
• BAT2: BAT2: an Open-Source Tool for Flexible, Automated, and Low Cost Absolute Binding Free Energy Calculations
  
• 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.