Rescoring of molecules with 3D SB scores

Molecules can be docked and rescored using the 3D structure-based (SB) scores computed by Makya's 3D Structure-based module:

1. The Docking Score;
   • in post-processing rescoring, unlike during generation, docking is unconstrained. RMSD to the reference ligand is not computed. Please note that a reference ligand is still required to find the binding pocket and set up the Contact Score. 
2. The Contact Score.

NOTE:

• Scoring with 3D scores leads to extra billing costs, because of the computing costs associated to the calculation of such scores.
• Scoring with 3D scores is not instantaneous, and results may take up to ~ 100 minutes to be computed (see the Generation process and runtime graph in the following page).

Important restrictions

Because of the additional computing costs associated to 3D SB rescoring,

• Scorers with 3D SB scores cannot be associated to a generator;
• Rescoring is limited to datasets of maximum 1000 molecules. 

Creation of a 3D Structure-based scorer

To rescore molecules with 3D SB scores, you first need to create a scorer that computes your 3D SB scores:

1. create your 3D structure-based settings,
2. create a new scorer,
3. select the 3D SB settings you want to use in the section "Iktos Scores". 

Rescoring of molecules

Once your scorer is created, you can select the molecules you want to rescore. Rescoring is limited to datasets of maximum 1000 molecules and can take up to ~ 100 minutes, depending on the size of the dataset.

The steps to select molecules for rescoring are described in the following page: Scoring molecules in a dataset.

Once rescoring is finished, the dataset is marked as "Done" and saved as a Makya Dataset.

3D visualization of rescored molecules

Rescored datasets can be seen and exported as SDF files in the Datasets tab.

By clicking on "View 3D", users can visualize the docking poses of rescored molecules: