Ligand Docking - Active Learning Advanced Settings Dialog Box

The options in this dialog box define advanced parameters for hydrogen bond treatment, pose filtering, and energy adjustments used during docking in Active Learning mode.

To open this dialog box, click Advanced Settings in the Docking options section of the Docking Setup tab of Ligand Docking Panel while it is in Active Learning mode.

  • Features
  • Additional Resources

Ligand Docking - Active Learning Advanced Settings Dialog Box Features

Aromatic H and Halogen H-bonds section

These settings control whether aromatic hydrogens are considered to form hydrogen bonds, and whether halogens can form hydrogen bonds as acceptors or weak bonds with electronegative atoms (like oxygen) as donors. These bonds are treated like other hydrogen bonds: they are included in the rough scoring, in the final scoring function, and are considered for hydrogen-bond constraints.

Include aromatic H as donors option

Select this option to include aromatic ligand hydrogen atoms as donors during docking.

Partial charge must exceed text box

To be considered as a donor, the partial charge on an aromatic hydrogen must be greater than the value given in this text box. Only available when Include aromatic H as donors is selected.

Include halogens as option and settings

Select this option to include nonbonded interactions with ligand halogens. You can choose one of two possibilities for halogen interactions:

  • Acceptors (default) — Treat halogens as acceptors of hydrogen bonds.
  • Donors — Treat halogens as donors of nonbonded interactions with electronegative atoms, such as oxygen. This effect originates in the positive potential on the halogen in line with the bond axis (sigma hole).
Pose Filtering section
Coulomb + vdW energies (combined) cannot exceed text box

Reject poses with Coulomb-van der Waals energy scores greater than the specified cutoff (in kcal/mol).

Preserve archive of sub-job poses option

Select this option to keep an archive of the poses generated by individual sub-jobs, in addition to the merged output. This option is selected by default.

Energy Adjustments section
Reward intramolecular hydrogen bonds option

Select this option to reward intramolecular hydrogen bonds in the ligand during docking.

Enhance planarity of conjugated pi groups option

Select this option to apply a penalty for nonplanarity in conjugated pi groups, such as biphenyl.

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