| Input preparation |
Crystallographic waters within 3.0 Å of protein and ligand are included in the docking study |
| Ligand Translation |
Ligand moves up to 5 Å, finding a non-clashing location. |
Ligand & water move together up to 5 Å, finding a non-clashing location. |
| Water Translation |
Up to 50 cycles of 1 Å water movement, first non-clashing move is accepted. |
| Ligand Rotation |
Ligand rotates up to 1000 times to optimize attractive & repulsive scores |
Ligand & water rotate together up to 1000 times to optimize attractive & repulsive scores |
| Water Rotation |
Waters rotate together up to 100 times to optimize attractive & repulsive scores |
| High Resolution docking |
6 Cycles of ligand & water translation (0.1 Å) and rotation (5°). Each cycle coupled with side-chain rotamer sampling & gradient based minimization of side-chain and ligand torsion angles. |
| Final minimization |
Gradient based minimization of backbone and side chain degrees of freedom around the ligand and waters. |
