Docking

MolModa's docking workflow predicts how small molecules bind to a target protein, returning both a pose (geometry) and an affinity score. Docking is run from Binding Docking Compound Docking/Scoring (guided tour).

For a step-by-step walkthrough, see the TD001 tutorial.

Preparing for docking

Before running a docking calculation, you typically need to:

1. Load a protein (Protein Data Bank, AlphaFold, or a local file) and a set of compounds (PubChem, file, text, or the molecular editor).
2. Protonate the protein and the compounds at the relevant pH (Proteins Protonate/Deprotonate Proteins (guided tour); Compounds Build Protonate/Deprotonate Compounds (guided tour)).
3. Identify a binding pocket (Proteins Pocket Detection (guided tour)) or define a custom region (Regions New Region (guided tour) or Regions Region From Molecule(s) (guided tour)).

Analyzing results

After docking, two analysis plugins help you interpret the output:

• 2D Interaction Diagram (Binding Analysis) (guided tour) — generates a PoseView diagram showing protein-ligand interactions for a selected pose.
• Evaluate Docking Performance (Binding Docking) (guided tour) — calculates receiver-operating-characteristic (ROC) and enrichment-factor curves, useful for benchmarking a docking protocol against known actives and decoys.

Docking scores and poses are organized in the Data panel, where you can sort, filter, and select entries for closer inspection.