NovaDock wizard: Options

When you predict protein docking with NovaDock, 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 Structures 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.

• rmodes – Number of normal modes of motion to explore for the receptor. We suggest using the default (5) to model large, concerted conformational changes and using a higher number (e.g. 20) to model more localized fluctuations, such as within antibody interfaces.

• lmodes – Number of normal modes of motion to explore for the ligand. We suggest using the default (5) to model large, concerted conformational changes and using a higher number (e.g. 20) to model more localized fluctuations, such as within antibody interfaces.

• ncopies – Number of copies of each swarm point to run. The default is 4.

• rcontacts – To list proposed contact residues for the receptor. This causes NovaDock to focus docking around the specified contacts, reducing computation time. Each line represents one contact residue using the format: [CHAIN ID][RESIDUE NUMBER]

• • The CHAIN ID is case sensitive and is typically a single character.
    
    
  • The RESIDUE NUMBER is an integer and may include an insertion code.

Examples:

R 15
R 15A

As an alternative to typing in proposed contact residues, you can click the “choose a list” link to navigate to a file containing a list of contacts.

• lcontacts – To list proposed contact residues for the ligand. Each line represents one contact residue using the format: [CHAIN ID] [RESIDUE NUMBER]

• • The CHAIN ID is case sensitive and is typically a single character.
    
    
  • The RESIDUE NUMBER is an integer and may include an insertion code.

Examples:

L 15
L 15A

As an alternative to typing in proposed contact residues, you can click the “choose a list” link to navigate to a file containing a list of contacts.

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