Protein - Protein Docking Beginner Tutorial

[@twinbrothers111]

Extremely informative

[@Bioinformaticswithbb]

Glad it was helpful!

[@rahulhazari9212]

Thank you so much sir. I am a phd student and just started learning about docking. I am very much delighted learning this way from a fantastic teacher like you. Please let us when the advanced session is coming.

[@Bioinformaticswithbb]

So nice of you.. Soon

[@yoatzinpenaflor1262]

Excelent video! Hope to see part two soon!

[@Bioinformaticswithbb]

Coming soon!

[@moh619]

Hey There can you please create a playlist for the videos... the newer ones... it will make it much easier for us to navigate and follow the lectures serially.. THANKS SO MUCH!!!!!!!!!!

[@31rifahnoorchowdhury19]

How can i dock two protein if one of those protein is bound with a ligand small molecule?

[@Jun_kki]

Sir, please share the link for the advance one, I am unable to find it.

[@SJR-2024-JJ]

Hi. I wonder if there is any software can predict the binding affinity for existing protein (already know which side of the protein interact with the peptide) with a 20-30 amino acid peptide??!

[@Jun_kki]

Sir, could you please suggest a way by which i can so multiple protein protein docking at once as i want to dock different proteins with one protein.

[@theshillonggirl]

Thank you so much . please could you also made a video on how to interpret the interactions? the scores or something how to determine whether it is interacting

[@Bioinformaticswithbb]

Check my video on Advance Pymol Tutorial

[@Zhou-n6y]

Hello, how does HEX do macro docking? I need your help.

[@李若颖]

why can't I save the final complex in hex docking

[@diptenl]

Sir, thank you for this informative video. Please make the 2nd part of it and also explain how to show the residual interactions in publication.

[@shuvronilchakraborty8163]

Where I can find the chain number information

[@TALKyLIKEENGLISH]

Thanks for your help

[@AdnanAli-mr4yz]

I need your second video which you are mentioning in the video

[@YangalaSudheerBabu]

Dear sir can you please teach me separately in Google meet for downloading the structure of protein protein interaction??

[@sanjaykumarpaul1864]

Sir...what if the two protein dont interact? How the result will be displayed,?

[@subhadipsaha5457]

Sir everytime I try to open a cluspro docked file in pymol it says invalid selection name " model 000.01". Can you please let me know the reason? THanking you

[@naveenlouis5197]

Thank you so much for this helpful video Prof :)

[@MashiDani]

3h42 and 3m0c are in complex. did you seprate them before?

[@sharavanakkumarsk5367]

How can you perform docking in HEX without using a complex file, the performed docking doesn't have any significance without it, where are the RMSD values, it should be below 1.

[@Bioinformaticswithbb]

Ur question is not clear, As any other docking program hex also accept one receptor and ligand molecules. Regarding ur RMSD question, Hex uses docking confirmation to identify and hence superpose corresponding pairs of alpha-carbon atoms from each chain in order to calculate RMS deviations between the docked position of the ligand and its position in the known complex. Unfortunately, there was an error with calculation of these values in HEX, for every docking results it will show is as RMS=-1, which i feel not accurate, that's y hex was not approved by CAPRI committee. But still i feel, with FFT algorithm i got better results compared to other docking algorithm.

[@sharavanakkumarsk5367]

@@Bioinformaticswithbb Yo, If it shows -1 as RMSD which means the docking is not performed correctly. Actually I want to say that you have to use a complex protein file, which is the one used to calculate RMSD, It should be around 1. As you said hex superimpose corresponding pairs of alpha-c atoms with respect to the alpha-c atoms in the complex protein file. There is a also a option named complex. Better look at it

[@Bioinformaticswithbb]

@@sharavanakkumarsk5367 for that reason Hex not validated in CAPRI ... as i told u my experience, i tested with some experimentally proven structures, and docking poses are mostly accurate

[@Jun_kki]

Sir, I want to do multiple protein docking. Is it possible via this?

[@MashiDani]

why did you use hex when it was non validated

[@amalamol7893]

Thank u so much for this information.Can we predict putative interactiing partners? If no reference is available?

[@carlosd.3489]

How do you combine the two ClusPro subunits into one, to display files as Hex?

[@carlosd.3489]

I wanna see the interactions, but I can´t...

[@lilinito9510]

A great tutorial video. Thank you so much Please how much time it tooks to get results?

[@mohammednashith3037]

how to find the binding energy in the docking?

[@mahadevbodake3344]

Will u z make vedio about pydock web

[@Bioinformaticswithbb]

Soon

[@SufyanKhan-qv4js]

Hello sir very informative video. Sir, I want to dock wild-type and mutant RBD of Omicron Spike protein with ACE 2 receptor by cluspro. How can I do that? Please kindly ASAP. Thank you! Sir, also I have a macromolecule ligand 2s albumin and a model ligand flocculating protein and want to dock it with the mutant RBD Omiron S-protein-ACE 2 complex. How can I do that?

[@twinbrothers111]

Plz tell us about the software

[@asiti2000]

hi sir. a good video. can you have a video on the preparation of the molecules before you can dock them using cluspro or any other software? or we can just use the molecules we downloaded from protein data bank as it is?

[@sayakroychowdhury1954]

Please provide the tutorial to further analyse the doxking results and visualize the interacting residues. Needed urgently😭

[@Bioinformaticswithbb]

Soon

[@universefactspluse]

Very informative

[@Bioinformaticswithbb]

Glad it was helpful!

[@alcides8737]

Parabéns!

[@biryani6861]

sir wonderful information, sir please can you explain glawxyweb for peptide protein docking

[@manukupani4771]

Hi...very informative video...could you please upload a video on RNA seq analysis.

[@Bioinformaticswithbb]

Thanks ... Soon

[@ddeonu5695]

General Queston: Why is Protein - Protein Docking important?

[@AmruMagdy]

ربي اغفر لي ولوالدي وللمؤمنين والمؤمنات والمسلمين والمسلمات الأحياء منهم والأموات.. 147