Ligand AIDE is a de novo ligand generation workflow based on Artificial Intelligent Design Evolution. It uses an iterative evolutionary strategy to grow and optimize ligands directly in the context of a protein binding site.

To run Ligand AIDE:

• Setup the Docking project.
• Docking -> De Novo Tools -> AI Ligand Generator
• Enter the name of the Docking project.
• Enter the Number of Generations. This option controls the size of the result ligand. Default (4) is generally for mid-size ligands. For large pockets the value can be increased.
• Enter Ligand Population number. This option defines how many ligands are retained and evolved in each generation, balancing chemical diversity against runtime.
• Enter the Min Synthesizability cutoff. Sets the minimum synthesizability score required for ligands to survive selection, enforcing practical synthetic feasibility.