Analysis of Docking results by Autodock ||Protein Ligand interaction || High Quality 2D & 3D figure

In this video Tutorial I have explained how to analyse Autodock results using PyMol, chimera, Maestro and Online server like PDBSum, Protein Plus and PLIP (Protein Ligand Interaction Profiler). Molecular docking is one of the most frequently used methods in structure-based drug design, due to its ability to predict the binding-conformation of small molecule ligands to the appropriate target binding site.

[@ET-bv4eu]

Wow! What a tutorial.... Thank you so much Sir! JzkAllah

[@MuzzammelRehman]

Thank you

[@ProfessorRehmanShahzad]

Masha Allah great manof Bioinformatica

[@hamzaali-ni8qg]

You are amazing sir explaination is very clear in all lectures

[@dariastr9892]

Thank you very much for this tutorials, quite detailed and very useful and helpful

[@MuzzammelRehman]

Thanks. Like and share with others to promote free learning

[@wajeehanoor5503]

Great video Sir. Thanku for commutative information and analysis.

[@mohamedbelazreg9949]

Tanks to you Sir, this is a great video

[@jyotirasgania45]

Amazing sir....this tutorial was very helpful

[@hodamando3296]

Excellent tutorial

[@MuzzammelRehman]

Thank you

[@MuzzammelRehman]

Also share to others who want to learn these things free of cost

[@MohammedAminu-m8e]

Hello Dr. Rehman,
Thanks for the insightful video. Please I am Mohammed from Ghana. I am using AutoDock Tools, AutoDock Vina and DS visualizer. When I do the docking, the ligand breaks at the rotatable bonds of the ligand. This makes it difficult for me to calculate RMSD and only one section of the ligand shows in the 2D diagram viewed by 2D visualizer. Please is there anything I am missing.
Thank you.

[@rohitchel5679]

Im performing docking on a known active site so i limited the gridbox around the active site only. Some of the conformations i got after docking were outside the grid box. Is that normal?

[@drittepushpavathi8057]

Thank you sir for valuable session

[@user-rm4rp6lg4p]

Hello sir
How i can docked of coordination complex with protein

[@YTantirungrotechai]

big thanks!!

[@MuzzammelRehman]

Thank you dear

[@sbkcs]

Excellent turirial masha alla

[@MuzzammelRehman]

Thank you

[@sanjaisrao484]

Sir if I upload my docked complex in chimera, its not showing the ligand sir...what to do?

[@MuzzammelRehman]

firstly open it in pymol and then save it in pub formate then open in chimera

[@jyotirasgania45]

Thanku so much sir🙏

[@Krishna-qo6rx]

Sir in pose view, its coming failed in ligand extraction what to do?

[@MuzzammelRehman]

How did you proceed?

[@Krishna-qo6rx]

@@MuzzammelRehman Sir I uploaded docked complex from autodock4 result in protein plus
After I uploaded the ligand was not in the pocket as u had shown,it was far.And after i clicked calculate its showing ligand extraction failed try again

[@MuzzammelRehman]

@@Krishna-qo6rx open the output in Pymol and then export that as PDB then you will be able to proceed it further or you are doing some mistake in docking ,then, follow my tutorial of docking . Again do the same as open the output in Pymol and then export that as PDB then you will be able to proceed it further

[@hodamando3296]

Does these steps apply to Autodock 4?

[@MuzzammelRehman]

Yes for sure

[@redscorpionas87]

Nice job Sir. but how can I transfer file to .dlg. Also I have to choose ligand file after DFT optimization or before? Thanks in advanced

[@jaishreemali9443]

Can we get autodock for free online?

[@MuzzammelRehman]

You can use online server for docking . There are many servers , i will upload tutorial on them as well

[@harper8994]

You didnot give reasoning or significance of the steps you did. No explanation what is drug score, what value should it have. Only the technical work you are explaining which is easily available over the internet. Please give in depth explanation for your steps, not only just changing colors in the video

[@harper8994]

What you are explaining is what we can see on the screen. We expect scientific explanations for God’s sake