I am trying to see whether there is an interaction between a specific virus protein and a natural compound (which will serve as my ligand), however I have no experience in molecular docking. I am aware that there are certain steps that need to be undertaken for me to get my protein and ligand both ready before I run molecular docking, but I am not sure where to start or how.
Some guidance would be very much appreciated. Thank you in advance.
Nikhita Peswani Hi
First of all, you should go through the literature you have targeted for study and find out the reactivity of residues that are involved in catalytic properties. As you said you are a beginner so every software has its own methodology for docking. Here I am attaching some links of articles
Article Computational Study Reveals the Inhibitory Effects of Chemic...
Article In-silico Study to Identify Dietary Molecules as Potential S...
Article Exploration of Luteolin as Potential Anti-COVID19 agent: Mol...
Article Bioactive components of different nasal spray solutions may ...
Article Drug Repurposing to Discover Novel Anti-Inflammatory Agents ...
I hope it would be help in your study
Your question is not clear enough but from how I understand it, I think you have to minimize their energies before proceeding to docking
Mam,you may download chimera tool.It is a free software easily available. There you will find everything that is needed to prepare a protein or ligand for molecular docking.
It is difficult to give a reply in one or two sentences.It requires hands on training.
videos are available in youtube please watch it. OR
S N college,Kollam,University of Kerala,India is conducting a certificate course in CADD. Surely it will help you.If you send your mail id I will send the details about the course.
You'll need to have files for both ligand and receptor through either .pdb or .mol2. These are the same files that allow you to visualize through software like chimera. In chimera there is a tool for "dock prep" this will add hydrogens and charges to protein and ligand. These are the very first steps, for more information you can easily find guides online for whichever software you want to use.
https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.html
In my opinion the simplest way is to apply the LigPrep and the Protein Preparation modules in Schrodinger (licensed).
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