Free Energy Calculations

ABFE

• A3FE: Automated Adaptive Absolute Binding Free Energy Calculations

• ABFE_workflow: Automated Absolute Binding Free Energy Calculation Workflow for Drug Discovery
  

  

• 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
  

  

Accelerated

• CS-FEP: combined-structure free energy perturbation
  

  

• Multi-eGO: Estimation of Ligand Binding Free Energy Using Multi-eGO
  

  

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

• 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.
  

  

Active learning

• FEgrow: An interactive workflow for building user-defined congeneric series of ligands in protein binding pockets for input to free energy calculations.
  

  

Guides

• Best Practices for Alchemical Free Energy Simulations:
  

ML-enabled

• ATM_with_NNPs: Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials
  

  

• QuantumBind-RBFE: Accurate Relative Binding Free Energy Calculations Using Neural Network Potentials
  

  

RBFE

• SPONGE-FEP:
  

  

  

Thermodynamics Ensemble

• DynaFormer: deep learning model to predict the binding affinities based on dynamic protein-ligand interactions

  

Tools

• 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.
  

• 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.
  

  

• PairMap: Intermediate Insertion Approach for Improving the Accuracy of Relative Free Energy Perturbation Calculations for Distant Compound Transformations
  

  

• alchemlyb: simple alchemistry library
  

  

• gufe: GUFE is a toolkit for developers of software related to alchemical free energy calculations, containing data models and abstract base classes.