8.9 Evaluation of the interactions (docking score analysis)

In order to analyze the docking results, you can calculate the interaction energy between a ligand and a biomacromolecule, evaluating the contributes of each residue that can be shown in the graphic environment. This function is available by choosing Calculate Interactions from the main menu.
To calculate one or more docking scores, you must select the ligand, typing its molecule number in the Ligand field or clicking on the ligand in the main window.

 

Evaluation of the interactions

 

The Dielectric (dielectric constant) parameter is used in the electrostatic energy evaluation only (Electrostatic and Electrostatic distance dependent) and the Cutoff  field defines the maximum distance between an atom pair over which the contribution is discarded.  You can select more than one or scoring functions as shown in the following table:

Scoring function Description
CHARMM R6-R12 R6-R12 non-bond interaction evaluated by CHARMM 22 force field provided by Accelrys. To perform this calculation, the parm.prm file must be copied in the ...\VEGA ZZ\Data\Parameters directory. This file is not included in the package for copyright reasons.
CHARMM 22 R6-R12 R6-R12 non-bond interaction evaluated by CHARMM 22 force field.
CHARMM 36 R6-R12 R6-R12 non-bond interaction evaluated by CHARMM 36 force field.
CVFF R6-R12 R6-R12 non-bond interaction evaluated by CVFF force field.
Electrostatic Electrostatic interaction.
Electrostatic distance dependent Distance-dependent electrostatic interaction.
MLPInS Hydrophobic interaction calculated using the Broto's and Moreau's atomic constants.
MLPInS square distance Hydrophobic interaction in which the distance between interacting atom pairs is considered as square value.
MLPInS cubic distance Hydrophobic interaction in which the distance between interacting atom pairs is considered as cube value.
MLPInS Fermi's equation Hydrophobic interaction in which the distance is evaluated by the Fermi's equation.

For more information about MLPInS, click here.

 

Checking Best residues, the residues with a partial interaction energy greater than Threshold (%) of the total energy are shown in graphic window.  If more than one scoring function is selected, it will be impossible to show the best interacting residues in the main window. Checking Worse residues, the residues with the worse energy contribution are shown. Checking Consider selected atoms only, the active (visible) atoms are considered only in the calculation and checking Copy the results to clipboard, the evaluated energies are copied to clipboard. This feature is useful to paste the results to a spreadsheet (e.g. Microsoft Excel) to elaborate them.
Your can modify the visualization choosing the colouring method (Ligand by atom, By molecule, By residue and By residue energy) and which residues to show (LigandBest residues, Worse residues and Water molecules).

An output example is shown below:

Interactions   Cyan = best residues
  Red = worst residues
  Green = ligand

 

WARNING:
To evaluate the interaction energy, you must follow these rules: