Prepare your own Pocket Exploration¶
To prepare your own pocket exploration to obtain putative binding sites of your small molecule and retrieve the most promising binding modes of yout ligand, please follow the steps below.
Input (further explained below):
Protein-ligand.pdb
Output (further explained below):
Most promising pockets ranked
Most promising binding modes ranked
Computational time: 24h
1. Complex Preparation¶
Prepare the system with maestro (Protein Preparation Wizard) and output a complex.pdb. The complex.pdb must contain protein-ligand. The ligand can be place anywhere as it will be automatically placed all around the protein by our automatic pipeline.
Make sure the ligand has:
Unique chain
No atomnames with spaces or single letter
Any residuename except UNK
2. Input Preparation¶
Prepare the input file input.yml
:
Pocket Exploration (24h)¶
system: 'docking2grid6n4b_thc.pdb'
chain: 'L'
resname: 'THC'
seed: 12345
#Distance to track along the simulation
atom_dist:
- "A:2:CA" #First atom to make the distance to
- "B:3:CG" #Second atom to make the distance to
allosteric: true
For more optional flags please refer to optative falgs
3. Run simulation¶
To run the system launch the simulation with the next command:
python -m pele_platform.main input.yml
4. Output¶
Best pockets ranked by ligand energy:
working_folder/refinement_simulation/results/clusters
Best snapshots ranked by ligand energy:
working_folder/refinement_simulation/results/BestStructs/