I appreciate your informative and simple guide. I request your instructions via a tutorial video on how to dock heavy metal ligands (like Palladium oxide or Silver) to a protein using Autodock 4.2.
Ur videos are great sir! Its very useful and the explanation was so good. Please make some videos about protocols of protein-ligand interactions and about schrodinger software. Thank you!
Thank you for your feedback Ashwin ! I currently do not have lisence for accessing Schrodinger software. How ever, I am planning to make a video on DiscoveryStudio & AutoDock softwares for protein-ligand docking. Hope those topics will be useful for you.
Sir please upload one video for docking for knowing the blinding interaction between protein protein (gene-gene) interaction 8n autodock ..is it possible in it?
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
Thank you sir. it is very much helpful. Sir, if we are taking protein and ligand separately( protein.pdb and output.pdbqt), and trying to find [action-preset-ligands] , i am getting the polar bond for the whole protein, how do i do to get the polar and non-polar residues only nearby the ligand?
Hi Nidhi, You have to use the Original Protein.pdb file that you have given as input. If the protein structure has other heteroatoms, like Water Molecules, and othe co-crystallized molecules, this issue could occur. It can also occur, if you use the protein molecule as protein.pdbqt which is taken from the AutoDock output folder. If this is not the issue, then see if the protein structure is having any issues. Let me know if it resolved.
When we require to find the binding site residue, do we have to consider only the residues involved in polar interaction or both polar and non-polar? Pls do reply sir.
hello, if i have to compare the functiom of inhibition of 2target cell from inhibitor, what i have to do?? i already get each protein~inhibitor complex, how can i compare these 2 complex??
Hi Ankita, I have already made a video for the same. Plz check the channel for other videos. ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-49q1w0EuuhU.html Identifying Binding Site on Protein : Tutorial Hope it helps.
