I would say the first and most important aspect of analyzing docking results is to thoroughly understand the protein you are studying. The data obtained from structure-based methods is easier to interpret with some knowledge of how (and where) the protein interacts with substrates or inhibitors. You can find this information in the PDB by checking experimentally obtained structure-ligand complexes of your protein (additional discussion is usually available in the respective papers). Mutagenesis studies are also useful when available, as they assess the importance of specific residues.

Additionally, it is good practice to run a redocking with the protein (i.e., docking a ligand for which an experimental pose is available, like the complexes mentioned above). The objective here is to determine if the docking protocol can adequately reproduce the "real" conformation for the system you are studying (since docking accuracy varies depending on the protein). Typically, the RMSD between the original and docked conformations is calculated to assess this "reproducibility," measuring how much they deviate from one another (the lower the number, the better the fit between them).

For interactions, there are plenty of options. The PLIP website (https://plip-tool.biotec.tu-dresden.de/plip-web/plip/index) is convenient because it runs in the browser and checks for several types of interactions (including halogen bonds). Discovery Studio and Maestro (the academic version is free) are also useful options, with tutorials available. One way or another, you will need to know which types of interactions are relevant for the protein in question (hence the necessity of exploring the literature a bit first).

I hope this gives you some clarity on where to start. Please let me know if you have more questions.

Best regards, and good luck!

Dear Badr-Ddine El Mouns .

Interpreting and analyzing molecular docking results involves several key aspects, including evaluating binding affinities, analyzing binding poses, and understanding the interactions between the ligand and the target protein. Here’s a proposed guide (that I personally use) to effectively analyze your results:

1. Binding Affinity

• Understanding ΔG: The binding affinity is often represented as a free energy change (ΔG). A more negative ΔG indicates a stronger binding affinity, suggesting that the ligand binds more tightly to the target protein. Conversely, a less negative or positive ΔG suggests weaker binding.
• Comparing Ligands: When comparing different ligands, look for differences in their binding affinities. A significant difference in ΔG can indicate which ligand may be more effective at binding to the target.

2. Root Mean Square Deviation (RMSD)

• Definition: RMSD is a measure of the average distance between atoms of superimposed proteins. In docking studies, it is often used to evaluate the stability of the docked conformation compared to an experimental structure.
• Interpreting RMSD Values: Lower RMSD values (typically
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That's a great advice and we really appreciate your guidance on interpretation of Molecular Docking