Molecular Docking VINA | Script Based Method | Multiple Ligand Docking

Please do keep making this type of videos it's very helpful

Hello, thanks a lot for the video. I got one issue with my rankings. When I dock 500 molecules in my VS set, and I need to sort all docked molecules by the number. I end up having ~20 molecules with same score..because Autodock provides only 1 decimal number. How do I know among 20 which one is ranked better than the other etc?

Thank you for the tutorial, can we just choose the repair the missing atom in the autodock tools options instead of build model from PASTA sequence for repairing the missing atoms?

Thanks so much for sharing this video. I have a question. I tried to use a command “obminimize” with my sdf files or mol2 files but it seemed to work with the first molecule only not every molecule that we want.

Thankyou for this tutorial, I was wondering if you can make tutorial on the updated VIna 1.2.3 version with latest features it is offering

Thank you ❤️ for making this video it solved my doubts about docking multiple ligands.

Very informative video! But i have one query. While converting .pdb files to .pdbqt files using obabel command, most of the hydrogens are missing along with some other heteroatoms. But when i convert them using autodock tools, its working perfectly. Is there any way to convert them using autodock tools with just one command? Please help. Thank you.

That is an excellent video. I'm really really thanks for it.be a successful and happy, dear doctor

Worked😄Thank you so much!!!

Hi there, great tutorial , I wanted to ask about how could'nt get the wildcard *.sdf to work in >obminimize -ff MMFF94 -n 1000 *.sdf and have to minimize my ligands one by one. Is it something particular to running obabel on Linux or could it down to the version of obabel you are using? Many Thanks Peter

How can you validate your docking method in Autodock / Autodock Vina. Normally, we perform docking process with co-cristalized ligand of crystal structure and calculate RMSD value. If it is less than 2A we can accept that our docking method is good. In autodock we get different rmsd values, reference rmsd and cluster rmsd etc. In publications how'll we state the validation of our model?

Sir how we can dock a rigid protein and multiple flexible proteins at once. Waiting for your reply.

Thank you so much dear BB, I raised my query in previous video and got my answer from this current video. Now it will be very easy to analyze the results.

Thankyou very much , it was so useful

Thanku so much again for this wonderful session.

Hi I want to do simultaneous multi-ligand coupling calculations in Autodock4. I have read articles on MLSD but still don't understand how to do it, it is confusing. Any advice? is there a protocol? Help please!!

Thank you for the freat video. what do you do if you have multiple ligands and multiple receptors? would you please share the script? Thank you

Hi Sir, I downloaded sdf files from ChMBL and not able to split them into several files. Do you provide any specific tutorial on payment basis. I want to learn virtual screening for my PhD (such as using Zinc database). Kindly provide your detail so that I can contact you.

it's very helpful thank u!

Thanks a lot, these videos always really help. Interestingly, I can't find a good tutorial for docking two ligands at the same time: A heme group, and an enzyme substrate for p450. This is different than what most people ask. It seems most people want to try many ligands to see which one is the "best". What I would like to do is take my p450, dock it first with a heme group, then dock the whole structure (p450 + heme) and dock it to a ligand. I managed to dock the heme group alone to my p450 using autodock vina in UCSF Chimera. But when I run docking simulations, I am only allowed to choose one receptor (either the heme, or the p450). The obvious problem is that autodock vina then attempts to dock the ligand to the p450 while ignoring the heme group. Any advice on this? Thanks!