NovaDock AI wizard: Options

When you predict protein docking with NovaDock AI, the second wizard screen is Options. This screen allows you to edit or specify prediction options. During the prediction step, options specified in this screen are applied to all docking jobs listed in the Sequences screen.

Edit or enter information in this wizard screen as desired. Or you can accept the defaults as they are, and simply press Next to continue to the Submit screen.

• Genetic database size – NovaDock AI constructs a deep multiple sequence alignment as input for the structure prediction process. Use the drop-down menu to choose either:
  
  
  • Extra large – To search through all 2 billion protein sequences in the full BFD.
    
    
  • Large – To search a reduced version of the BFD prepared by the AlphaFold group.

• Number of predictions per model – Choose any integer from 1-10. The default is 5.

• Trained network configuration – This menu has an unchangeable default of Multimer.

• Relax energy of models – Check the box if you wish to minimize the energy of the prediction. Leave the box unchecked to use the raw coordinates from the AI model.

• Use templates published until – Today’s date is shown by default. To limit templates to those published before an earlier date, specify the date by using the up/down triangles or by clicking on the Choose a date tool (). This option was designed for DNASTAR’s internal benchmarking purposes.

Click Next to proceed to the Submit screen, or Back to return to the Sequences screen.