Alchemical Free Energies

Alchemical Free Energy (AFE) Calculations

Calculating Absolute Binding Free Energies of Tyk2 Inhibitors
Building Simulation Boxes for ABFE Calculations (Tyk2)
Equilibrating Endstates in ABFE Calculations (Tyk2)
- Learning objectives
- Activities
  - Setting Up and Running End-State Equilibration
Determining the Boresch Restraint Contribution to the Free Energy
Creating Boresch Restraints for ABFE Calculations (Tyk2)
Generating and Running Lambda Windows for ABFE Calculations (Tyk2)
- Learning objectives
- Activities
  - Setting Up and Running Annihilation Simulations
  - Equilibrating the Lambda Windows
Analyzing ABFE Calculations (Tyk2)
Calculating Relative Binding Free Energies of Tyk2 Inhibitors
Soft-Core Potentials in Relative Binding Free Energy Calculations
- Learning objectives
  - Introduction to Soft-Core Potentials
- Relevant Literature
Network-Wide Analysis With FE-Toolkit
- Learning objectives
  - Introduction to Network-Wide Analysis
- Relevant Literature
Mapping Common-Core and Soft-Core Atoms in Relative Binding Free Energy Calculations
- Learning objectives
  - Introduction to Atom Mapping
- Relevant Literature
Merging Topologies for Relative Binding Free Energies
- Learning objectives
- Activity
  - Merging Topologies
Analyzing Free Energy Calculations with FE-Toolkit
The Python API for EdgeMBAR
Exploring FE-Toolkit HTML Edge Reports