Once your files (PDB and SDF) are prepared following the steps described in Preparation of the Input Files, upload them to Makya.
To do so,
- Go to the "Docking Files" tab;
- Click on New Docking Files;
- Enter a name for your 3D files, and select the docking tool you wish to use (a comparison of the scoring functions is given here); click on Next;
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Upload the two files:
- Protein in PDB format (without the ligand);
- Reference ligand in SDF format (co-crystallized, or previously docked)
- Specify if you want to use the water molecules present in the PDB file for docking (only available for rDock);
- Click Validate to proceed. You will be able to visualize the pocket and ligand in 3D.
Auto-preparation of 3D Files
Go back to the "Docking Files" tab. The files you uploaded are visible. You can then run Makya auto-prep by clicking on the Run button.
Makya auto-prep processes the 3D files for future use in Makya. For example, with rDock, it is possible to incorporate water molecules, cofactors, and metal ions into docking simulations. To do so, the preparation computes a docking grid before docking. rDock identifies the binding pocket using the reference ligand and then maps the cavity for docking.
This step is necessary to be able to use the files.