Molecular Docking using Chimera and AutoDock Vina

This video tutorial explains protein-ligand docking using Chimera and AutoDock Vina tool. The target molecule was retrieved from the RCSB PDB and ligand molecule from the NCBI PubChem database. Public URL for the sources and tools are below,
RCSB PDB - Database for macromolecules
www.rcsb.org/
NCBI PubChem - Database for small molecules
pubchem.ncbi.n...
Chimera - For molecule manipulation and visualization
www.cgl.ucsf.e...
AutoDock Vina - For protein-ligand docking
autodock.scrip... (OR)
vina.scripps.e... (OR)
github.com/ccs...
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KZbin Handle: / @akbit
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[@Estherlie1]

Thank you, the video was very helpful!

[@AKBIT]

Glad to hear it!

[@Estherlie1]

@@AKBIT Right now I‘m trying to save the protein with the docked ligand als pdb file, but I can only save either. Could you help me out?

[@AKBIT]

Watch this video kzbin.info/www/bejne/mn_bkGxreL9kesk

[@luismarioibarra2735]

Thank you for your tutorial, I just have one question, when I open the ligand file it automatically fits into the receptor, what could that mean?

[@AKBIT]

It is your perspective with the viewer. If you zoom in, you can find the difference. The ligand places the screen according to the atomic co-ordinates in the file.

[@sweetpie49]

Ashok sir... This was awesome

[@AKBIT]

Thanks for your feedback. 🙂

[@user-tc4dn9tg5y]

What are Gasteiger and Kollman charges? Where exactly are these charges being added in the protein? How can I determine the location of these charges in the protein

[@AKBIT]

What are Gasteiger and Kollman charges? Refer: expertcomputationalchemistry.blogspot.com/2016/08/the-difference-between-kollman-charges.html Where exactly are these charges being added in the protein? Refer page 5: www.csb.yale.edu/userguides/graphics/mgltools/UsingAutoDockWithADT.pdf How can I determine the location of these charges in the protein? Compare the protein before and after adding charges to find the difference. It will be present in the PDBQT file.

[@W_T24]

thank you its clear 😁😁

[@AKBIT]

You're welcome 😊

[@nihelos931]

Do we need to minimise the energy of ligand and receptor before running the AutoDock Vina?

[@AKBIT]

That is your choice. If so, you have to perform prior to docking.

[@professorswenson3504]

I do not see autodock vina as an option under tools and binding analysis. I downloaded autodock vina, but not sure how I get it to load into chimeraX

[@AKBIT]

Are you using Chimera or ChimeraX?

[@professorswenson3504]

@@AKBIT You are right, I was using ChimeraX. I am now trying to use PyRx for docking with ChimeraX, but it doesn't recognize my cxs file to open it.

[@AKBIT]

ChimeraX does not have an interface to AutoDock Vina program. UCSF Chimera and UCSF ChimeraX are two different programs; you would need to get Chimera to use this feature.

[@AKBIT]

If you are trying to use PyRx with AutoDock Vina, watch this video tutorial kzbin.info/www/bejne/fGiQY6FueNGVbJo

[@monikachaudhary9577]

Can you please share the autodoc vina program file used here or the download link for same

[@AKBIT]

vina.scripps.edu/wp-content/uploads/sites/55/2020/12/autodock_vina_1_1_2_win32.msi

[@AKBIT]

Installed programs will be at "C:\Program Files (x86)\Vina" directory.

[@AKBIT]

Latest release github.com/ccsb-scripps/AutoDock-Vina/releases/download/v1.2.3/vina_1.2.3_windows_x86_64.exe

[@clarissaayres2060]

ditch the music but great tutorial otherwise!

[@AKBIT]

Sorry! I am not expert in video creating. I'll try to do better next time.

[@su3rc]

Hme networks pharmacology sikhna hai

[@AKBIT]

Network pharmacology is the integration of various pharmacological properties (DiseaseProteinDrug) through molecular interactions.