Molecular Docking Analysis | Autodock Results Analysis | Protein Ligand Int | Pymol | LigPlot Etc.,

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Published 2020-07-18

This video give you a brief on Molecular Docking (Autodock) Results Analysis, in this we showed a tutorial how to extract various scores (Binding Free Energies, RMSD, inhibition constant (Ki) ) from Docking log file of Autodock. We also, shown how to generate 2D and 3D images using various web plot form.

Results Analysis Steps
1. Autodock Docking Log File Analysis
2. Save Best Docking Confirmation to PDBQT - In autodock
3. PDBQT to PDB - using Open Babel GUI
4. 2 D and 3D images - PLP, Protein Plus, LigPlot and Pymol

Autodock DLG file score Description:

1. Binding Energies:
bit.ly/397VNDt

2. Inhibition Constant:
bit.ly/32wfHGX

Tools:
1. Open Babael GUI : bit.ly/3eMgXZm
2. PLP web Server : bit.ly/30g07fS
3. Protein Plus Web Server: proteins.plus/
4. LigPlot+ : bit.ly/3fJ3see
5. Pymol pymol.org/2/

Literature :
link.springer.com/article/10.1007/s10822-010-9352-…
bit.ly/3h8Uffm

All Comments (21)

@prasanthfrancis1263 3 years ago

Thank you sir, you saved years for us.... I have searched for many journals and videos to understand how to analyse docking. This video and explanation is so clear. I have never found a video other than this which give complete explanation.
@lianbonnici5626 4 months ago

I have to write a very positive comment. Dear Dr. BB I highly appreciate for showing these tutorials. It makes our lives (non-bioinformatician experts) much easier as I can finally understand and replicate this for my own PhD project. Keep on making tutorials :).
@abdullahq.o7131 2 years ago

Really helpful video. Thanks a lot Doctor. This video and the previous one drastically change my status in my master project from knowing nothing in AutoDock to master it. I really appreciate your effort beyond making this video.
@adityanarayansahoo5397 11 months ago

thank you prof for your effort and dediacations towards new learners. also like to encourage you to providing this type of videos and wish your channel grow more and more .
@elhamabdel-badiea4998 1 year ago

Thanks for this comprehensive explanation for protein ligand interaction, the best video ever I have watched for this topic
@kasonk1692 2 years ago

GREAT LECTURE!!! THANK YOU SO MUCH!!!
@technologytransfer1952 2 years ago

wonderful explanations in very appropriate manner of video
@anandsingfattesingpatil5234 3 years ago

Thank you so much sirji. Very informative. Nice explaination. Simple language.
@sibbalaacademy9328 6 months ago

its cleared all my doubts in results analysis Thank you so much sir
@tanushreesingh1999 2 months ago

Thank you so much Sir for your noble service ❤
@kumargaurav2492 2 years ago

It’s really informative… thank you
@hirenmarvaniya7264 2 years ago

Very informative and helpful
@norm1124 2 years ago

Cobgrats to EXACTLY 10'000 subschribers 👍
@setyantotriwahyudi4322 2 years ago

Thank You Sir. Great Video.
@user-hw4cp1dt4p 10 months ago

thank you so much for the video
@bitajamshidi8103 1 year ago

Thank you very much sir. That was so helpful.🙏💐
@Pearl00Paul 2 years ago

Thank you for sharing! Did you ever figure out how to interrogate PyMol for the number/sequence of the protein residues that a ligand H-Bonds with? Other than manually selecting it via GUI, I have been looking for a way to do so via the command line in order to automate image generation for large data sets.
@hanstsahnang4533 3 years ago

best video. your channel is definitely my best thanks alot
@biomedicalscientistmuhammad 14 days ago

Exellent ❤
@1p53gen 3 years ago

very good explanation. Thank you so much.