Molecules scoring and filtering
Molecules generated with a 3D structure-based configuration are docked and scored using the Contact score and the Docking score. Molecules can be filtered in the Parallel Coordinates module and sorted using these scores.
3D visualization
By clicking on See details on any result, in the "Docking" tab, the generated molecule can be seen docked in 3D in the target protein binding pocket.
Interactions are indicated with dash lines. To see more information on a specific interaction, simply hover your mouse over the dash line: it will be highlighted in magenta and information will be displayed in the 3D visualization window (see image below).
To see the overlay with the reference ligand, check the Show Reference Ligand box above the 3D visualization.
By selecting several molecules and clicking on 3D Structure Based Results in the top-right "View" module, you can superpose all the molecules in the pocket simultaneously.
Export as a .sdf file
To export multiple molecules as a .sdf file, select the molecules and click on Export in the top-right "Selection" module. This will let you analyze and use the generated molecules outside of Makya.