The channel will post educational videos, tutorials, lecture videos on key subject topics for the benefit of UnderGraduatoin and PostGraduation students.
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
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?
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.
Sir could you please tell how to identify binding site a protein is not already bound with substrate or any small molecule. The crystal structure is also not available for my protein and I am using alpha fold structure. I want to perform protein-protein dockig and identify interacting amino acids among these proteins. Could you please help?
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.
please sir explain how can I set the grid box dimensions if the ligand I am trying to test (not the original ligand crystalized with the protein) lays far away from the protein (when I input the ligand to AutoDock 4)?? When I tried to cover both ligand and protein inside the grid, the grid box was very big which causes an error message to pop up may times.
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??
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.
i want to visualize a protein protein complex docked pdb file by zooming the specific binding sites for publication.I already did the binding in pymol.But when i try to zoom the binding sites into word the figure is not very clear to see.So kindly help me on this.Thanks in advance
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.
