Dear Nantenaina,

First of all, mention the protocol of preparing the receptor and the ligand. Secondly, for better elaboration and to aid the reproducibility of results, you must at least mention the following:

Dear Waqar Hussain

Thank you very much for your answer.

Now, could you ask me the parameters that could be required concerning the presentation of the results?

Dear Nantenaina Tombozara,

You may refer to any of my papers. I usually report binding affinity, along with Ki. Also, a graphical depiction of docked complexes by highlighting the interacting residues between receptor and ligand helps in understanding the results better.

P.S. I am attaching one of my studies.

Dear Nantenaina Tombozara,

We are working in the same research field. You can read our papers for your query.

Dear Waqar Hussain

Thank you very much for sharing your paper, it is a great help.

I have a big problem with the visualization of the residues involved in the interaction for the best score (the lowest binding energy).

How did you extract the out file containing only the best score and combine it with the protein in order to get the pdb file that will be used in Ligplot?

Dear Nantenaina Tombozara

You can choose the ligand of your choice out of all docked binding modes for that specific ligand through UCSF Chimera.

Dear Waqar Hussain

It is the first time I heard about UCSF Chimera software. Are their some tutorials concerning the manipulation of this software?

Dear Nantenaina Tombozara ,

You might find helpful information here.

https://www.cgl.ucsf.edu/chimera/tutorials.html