I am sorry to say that docking has only a limited possibility to underpin the biological activity of a molecule given the myriads of other factors involved, see for example:

Article Is Target-Based Drug Discovery Efficient? Discovery and "Off...

NO. Docking results won't describe any biological activity of a compound.... It will only interpret the molecular interactions between the protein and compound.....

If you want to predict the biological activity of the compounds computationally.... then you will have to do QSAR modelling to predict the IC50 values of the compounds......

Regards.

Approach to describing and interpreting the results of molecular docking:

1. Binding pose analysis: The docking software typically generates multiple binding poses, representing different orientations and conformations of the ligand within the binding site. Analyze the binding poses to identify the most favorable or energetically favorable pose based on scoring functions, such as binding affinity or energy.

2. Interaction analysis: Investigate the specific interactions between the ligand and the target protein. This involves examining hydrogen bonds, electrostatic interactions, hydrophobic interactions, and other non-covalent interactions. Identify key residues in the binding site that contribute significantly to ligand binding.

3. Binding affinity estimation: Docking programs often assign a scoring or energy value to each pose, which can be used to estimate the binding affinity. Lower energy or more negative scores generally indicate stronger binding. However, it's essential to interpret these scores cautiously and consider their limitations, as they may not always correlate perfectly with experimental binding affinities.

4. Validation and comparison: Validate the docking results by comparing them with experimental data, if available. This can involve comparing known ligand-protein complexes or experimental binding affinities. Assess the accuracy and reliability of the docking predictions based on their agreement with experimental findings.

Regarding determining the biological activity of a compound, it's important to note that molecular docking alone cannot definitively determine biological activity. However, it can provide valuable insights and hypotheses regarding potential ligand-target interactions. The docking results can guide further experimental studies, such as binding assays, biochemical assays, or in vivo experiments, to validate and confirm the predicted binding interactions and assess the compound's biological activity.

In summary, molecular docking results provide information about ligand binding modes, interaction patterns, and estimated binding affinities. While they can offer valuable insights into ligand-target interactions, experimental validation is required to confirm the biological activity of a compound. Molecular docking serves as a useful tool in the early stages of drug discovery and optimization, aiding in the design and selection of potential lead compounds for further development.

Hope it helps:credit AI