Good Afternoon !!
I am using Autodock Vina for protein-ligand study.I specified certain grid option and did the docking.
My concern is, in the output ligand file, there is ligand dimension which is not I defined in the grid option.
So is it blind docking?
Plz guide.
Hai Kapil,
I didn't get your question properly. You have specified certain grid positions while performing docking calculations using Autodock Vina. If your grid size (i.e. grid box dimensions) completely covers the entire protein surface area then it can be called as Blind docking. If you have any information of its binding site then you can reduce size of the grid box (i.e. reduce dimensions of grid) then it can be said as site specific docking.
I am unable to get this "in the output ligand file, there is ligand dimension which is not I defined in the grid option" line in your question, can you please elaborate on this. Then i can give more specific suggestions.
hello,
So in my grid box dimension, I` have chosen the binding site of the protein, but in the output ligand file, along with binding site region, the ligand was showing to interact other than grid box dimension.
PFA for more info.
I hope u got it.
Plz guide.
Hello,
I know the protocol to perform Autodock vina.
My doubt is,Plz check my previous answer,Also PFA the attachment ,hope u will understand my question.
Thank you
@Kapil: This can be a problem at times, when your ligand of interest has some charge. I have seen the image and In your case the corner input grid points (input Grid dimension corner coordinates) might have been closer the site where your ligand bound after docking. So, with its charges ligand might have found more affinity at the new site rather than your specified binding site on protein.
The possible solution can be to decrease the grid size bit more and re run the docking calculations again. I hope that can solve the issue.
All the Best.
Such that it cover whole protein of interest and also increase the exhaustiveness for better prediction.
- Badges
- Science topic
- Similar topics
- Biological Science
- Bioscience
- Biotechnology