To set-up the 3D structure-based scores, you will need to prepare two files to upload in Makya:
- The protein file of the target of interest, in PDB format - without ligand
- The reference ligand which has been co-crystallized or docked in the previous protein file, in SDF format
Protein preparation
Regarding the protein file, the data should be prepared as it would be for any docking software:
- Remove unnecessary co-factors and crystallization facilitators (GOL/SO4/PO4 ….)
- Remove unwanted water molecules
- Remove alternative positions
- Fix missing atoms of side chains
- Fix gaps when possible
- Do not cap the termini of chains
- Add hydrogens and protonate the protein at pH 7.4
- Remove the reference ligand
If you use third-party tools like MOE (CCG) or Maestro (Schrodinger), running a basic preparation without capping the termini should provide you with a good structure to use with Makya.
Reference ligand preparation
Regarding the reference ligand file: simply add hydrogens, protonate the reference compound in the binding pocket at pH = 7.4, and export the result as a SDF file.
Makya supports SDF file in the v2000 format. Files in the v3000 format are automatically converted to v2000.
Water molecules
With rDock (but not Vina), it is possible to incorporate water molecules, cofactors, and metal ions into docking simulations.
For docking with water molecules to be performed, water molecules must follow a specific format in the PDB file, ensuring correct atom naming for proper recognition during docking:
- Water molecules should be named using HOH in the HETATM section.
- Each water should have an oxygen atom (O) explicitly defined.
- Ensure proper occupancy values are set for flexible waters.
Example of correct format:
HETATM 997 OW SOL Z 997 -6.718 -25.016 20.117 1.00 0.00 O
HETATM 998 H1 SOL Z 998 -5.986 -25.627 19.980 1.00 0.00 H
HETATM 999 H2 SOL Z 999 -7.234 -25.108 19.304 1.00 0.00 H