Demo: Absolute Binding Free Energy (ABFE)
ABFE Calculation Workflow

Ligand-X Demo

Demo: Absolute Binding Free Energy (ABFE)

See how Ligand-X calculates the exact binding affinity of a single ligand to a protein target using rigorous alchemical methods.

Video Walkthrough

Coming Soon: Video walkthrough demonstrating the complete ABFE workflow in Ligand-X.

Data Flow Pipeline

When you submit an ABFE calculation, your data flows through these stages:

1. Ligand Preparation
  • Parse SDF/SMILES, add hydrogens
  • Assign AM1-BCC partial charges
  • Create OpenFE SmallMoleculeComponent
2. Protein Preparation
  • Parse PDB, clean structure
  • Create OpenFE ProteinComponent
3. Protocol Setup
  • Configure AbsoluteBindingProtocol
  • Set lambda windows (typically 11–20)
  • Configure HREX parameters
4. Complex Leg
  • Ligand bound to protein
  • Gradually "turn off" ligand interactions
  • Run HREX across lambda windows
  • Compute ΔG_complex
5. Solvent Leg
  • Ligand in water box
  • Gradually "turn off" ligand interactions
  • Run HREX across lambda windows
  • Compute ΔG_solvent
6. Thermodynamic Cycle
  • ΔG_binding = ΔG_complex − ΔG_solvent
  • MBAR analysis for optimal estimate
  • Error propagation for uncertainty
Results
  • ΔG binding free energy (kcal/mol)
  • Statistical uncertainty
  • Overlap matrices showing sampling quality
  • Convergence plots over simulation time
  • Replica exchange statistics

The Two-Leg Calculation

ABFE uses a thermodynamic cycle with two parallel simulations:

Image Description

Figure 1: Thermodynamic cycle for ABFE calculations

Tools Used

Stage Tool Purpose
Ligand Prep RDKit Molecule parsing, 3D generation
Charges AM1-BCC Partial charge assignment
Protein Prep PDBFixer Structure cleaning
Simulation OpenMM GPU-accelerated MD
Free Energy OpenFE AbsoluteBindingProtocol
Sampling HREX Hamiltonian Replica Exchange
Analysis MBAR Multistate Bennett Acceptance Ratio

Example Output

After calculation completes, you’ll see:

  • Binding Free Energy: ΔG in kcal/mol with error estimate
  • Overlap Matrices: Heatmaps showing sampling quality between λ windows
  • Convergence Plot: How the ΔG estimate stabilized over time
  • Replica Exchange Stats: Acceptance rates for configuration swaps
  • Thermodynamic Breakdown: Individual leg contributions

Protocol Settings

Parameter Default Description
simulation_time_ns 5.0 Production simulation per replica
n_lambda_windows 11 Number of alchemical states
equilibration_length_ns 1.0 Equilibration time per replica
n_replicas 11 Number of HREX replicas

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