How to Study Protein-Ligand Interaction through Molecular Docking

Presentation by Nehru V Sankaranarayanan, Ph.D. on Oct. 25, 2016.
Attendees will be introduced to molecular docking technology and will have an opportunity to work on a case study. Open source computational tools that can be used to study the interactions of protein-ligand complexes will be highlighted. A link to the case study handout is available at scholarscompass.vcu.edu/howtot... (scroll down to the bottom).
Part of "How-to Talks by Postdocs," a series of instructional brown-bag lunch talks for the general VCU health sciences community taught by postdocs. For more information, see About How-to Talks by Postdocs (rampages.us/howtotalks/about-2). For other talks, see scholarscompass.vcu.edu/howtot....

[@amosk.dwamenaphd.5047]

perfect recommendation for beginners

[@nurariffa3138]

This is extremely helpful, thank you!

[@skymoonrajan6531]

Thank you mam, for uploading a very useful video. It was very easy to grasp you flow of work

[@yanjundong3707]

Thanks for your help.

[@nosequiensea]

Excelent video, I want to ask how to know the best pose ? . You just have to count the number of H-Bound and check the distances ?. Another question, Do you know how to perform dynamic symulation with the docking results?

[@ebtihalabdullah3720]

can not express how thishelpful .... well and very clear informative explanation (Y) great job , thanks alot

[@Brain__Drain]

Excellent presentation, very helpful!

[@vivekanandinspire4883]

I think it will be good if you also share a video about simulation..that can be very helpful for study of this interaction in detail.

[@ritaasomadu]

Thanks for the video. Please, how do you adjust the grid box?

[@Rizw1Rex]

wow that was really helpful! 😇 Thankyou

[@nachiketmore829]

Respected Madam Thank you so much, the video tutorial has helped a lot. I had one query, How can we visualise the interactions of amino acids with ligands? May you please help?

[@candrakirana3959]

Good morning, i interested to watch this video, miss can i ask about the chimera??🙏🙏

[@arabindamahanty3382]

There is no demnostration of the autodock vina installation or application. COuld you please make a video for this

[@skymoonrajan6531]

Mam, your video was very useful and it helped me for my project

[@unays]

Could you please tell me, how I can study metal, like Cdcl2 or PlCl2, I been trying to do the same approach but sadly it's not working? could anyone help me how to sort out?

[@karnitin84]

While doing docking is described in an article, it prepdocks the ligand, but in this video the minimized structure command is used. Which one would be right? Doing both, minimized structure or dock prep option?

[@itooogure649]

can anyone tell me how to install vina? the profesor said that I needed to copy the files in Vina folder to molecular docking directory. what is it?

[@nutmitchiko]

Is it possible to do batch preparation using Chimera? We are using Marvin Sketch to generate the 3D conformers before loading in PyRx/Vina

[@pharmacyclass5075]

Can we do docking for multiple ligands with one protein molecule ?

[@hamzashukri5238]

Thank you for good presentation. can you help me for my docking study because no free online program are available /

[@marthachapa2401]

Hi, is this a docking with rigid protein and flexible ligand?

[@satinkorea]

The Autodock server is down. Couldn't download the autodock software. any help will be appreciated!!!

[@diptendusarkar1912]

how to do structural comparison by using this software?

[@dadasaheb12377]

How to download this software?

[@mepresident3750]

very useful video, like it

[@sattisuma6999]

Madam here showing receptor and ligand can not be the same model. Please can you suggest. Thank you madam

[@anjaneysharma1724]

its perfect.

[@mni79]

good work

[@shakirullah5570]

nice presentation

[@amelben5176]

it's very interesting, just a question, the translation, more explication please?!

[@corinbior9768]

Thank you ,but in 44:34 idont have vina.exe what i do or where i get it?

[@Rizw1Rex]

if you have some more video tutorial please provide me the link

[@balajinagarajan4190]

kzbin.info/www/bejne/r3PTaGeffbVsqKM

[@princyslifestyle2046]

mam I want to find out the interaction between the constructed synthetic gene with the cell surface marker protein, by which tool I can see the interaction

[@nawalsouadhalfaoui7136]

also interested to know more about that , if you've found something tell us :)

[@punit0031]

I am not able to get the results.

[@edthoreum7625]

12:20 docking, challanges

[@frostbites4314]

45:15 an error that says "too many heavy atoms (>100) in ligand" always appears just after I click ok. What should i do?

[@klauslubinus1433]

I've had this error before when I invert the selection of the ligand and the receptor.

[@ForeverHangry]

Same!! My thesis is due in a couple of days and I'm unable to resolve this issue.

[@MN-qz8ex]

If I use isomeric SMILES rather than canonical SMILES of a molecule, can CHIMERA tell the difference between two enantiomers?

[@carloseduardocastrozarate8939]

great but the auido was a little bad but no matter what it was amazing thanks a lot!

[@ThillaiNatarajan07]

In video 44:17 how to get autodock vena.exe file.. whether I have to install autodock software?

[@GauravSharma-ok4gz]

Yes, you need to install autodock software only for this, as a result it will automatically create a folder in "Scrips research institute" named folder in your computer. But, if you are not using chimera for ligand and receptor preparation, then you may need to download some additional tools like MGL tools.

[@unays]

In my case, my chimera, haven't auto doc vina? any suggestion.

[@Ehtisham101]

You will have to download auto doc vina, i think then chimera will show it.

[@DhanashreeLokesh]

I t was nice but at the end its appearing as shown below.Kindly help me to sort out. Running AutoDock Vina for 3erd.pdb failed; see Reply Log for more information Application stderr ----- 'C:\Users\Dhanu\Desktop\molecular' is not recognized as an internal or external command, operable program or batch file.

[@ranabirmajumder1840]

same here. Autodock running is failing again and again.

[@thequeenofitall2093]

I don't know if you tried to follow the instructions autodock.scripps.edu/faqs-help/tutorial/using-autodock-4-with-autodocktools/2012_ADTtut.pdf

[@thequeenofitall2093]

Anyways, it's easy to run autodock vina

[@thequeenofitall2093]

I can help you if you need it, btw I'm linux user since the software runs better in linux than windows, but it's a pain in the ass to install it haha

[@AmeerHamza-xs6xh]

how we can observe the interaction of cell wall with proteins like endolysins of bacteriophage

[@alimabbas4783]

i need software for the find out the interaction between biological molecules (protein, lipid and enzymes)and heavy metals (nickel nitrate)

[@thequeenofitall2093]

I think you (both) are asking for too much. In my opinion, it could be done with molecular dynamics, although I don't advise it since it's too much time consuming doing the animation for just a few femtoseconds (yes, you can only simulate that spending a long time haha)

[@mrzeshanhaider7713]

anyone can send me autodock vina scripts or how to donlod on window?

[@deyee111]

Zeshan Haider hello Dr. I am a post graduate student from Nigeria and I have a project on docking. u tutorial has really been helpful but I can't download the chimera from UCSF website to practice it. I av tried it severally but the website doesn't load at all. is there a way u can help send a downloaded copy to my email. [e-mail]

[@deyee111]

I prefer a windows copy cos I use windows

[@GauravSharma-ok4gz]

I think docking by autodock vina is more easy than in csf chimera

[@malasharma9738]

very nyc and informative video, but can u please share docking with a receptor with the library of compounds using Autodock Vina.

[@dodramswami4176]

Mala Sharma are u pharmacy student? How did u end up learning docking n how much u know?

[@Mo47123]

I tried everything as it has been shown here! But my run also failed too. 1. Then I have found that the link for Autodock Vina shared here was only for windows 32 bit and mine is 64!! Anybody, can you help me to get AutoDock Vina for 64 bit? 2. Another thing I have noticed while looking at the protein and the ligand that there is a big gap between protein and ligand (al least 3 times more protein sized gap). Pulling up together did not work as well. suggestions??? Thanks In Advance.

[@Karishmadaspurkayastharicha]

if anyone has step by step process written like a flowchart

[@izleyicia8915]

very good Thank u :)

[@Xx_Eric_was_Here_xX]

proteins.. i love the funky lookin little guys

[@annas9942]

Presentation is nice, just the sound is bad