Excellent video thank you 😊please make videos on how to select best pose and how to analyse the docking result and also on interpretation of results 🙂 very helpful video
Useful video just one question how do I add the Autodock to PyRx? I have downloaded both but the Autodock does not seem to be in PyRx as yours is? I have no 'vina executive mode' display. Thank you.
Some pdb structures already have ligand in them so to dock our desired ligand with protein should we need to remove the already existing ligand on protein or not sir.
Hello dear, I am using the free version of PyRx software dedicated to autodocking and virtual screening. After docking when I visualize the results as H-bonded residue of macromolecule in 2d interaction figure in Discovery studio visualizer. But every time, H-bonded atoms of macromolecule are not the same as given in research articles already published in the well-reputed journal. And I am following the same step as per the protocol and unmatched interaction is shown in docking and published papers. so kindly help me in this problem. thank u in advance.
Again a great content sir, always different from others. Learnt so much from you. Sir can you upload one class on how to view the vina docked results on Chimera? N I also asked you how to find out the binding sites of proteins like 3dei or 4ehk. Thank you🙏
@@crkphy Actually sir, Discovery studio visualizer is not accepting co-ordinated water molecule in case of metal complex , hence can't see 2D structure.Someone told me to use Chimera for this.
sir, during selection of macromolecules when sir select native ligand so how to know which native lig. we select for docking with our ligand or drug molecule? 2. when we select native lig. it's means we select binding site for docking? 3. if it's really binding site then in PDB protein they already define binding area by attaching ligand we have to just remove their lig. & attached our own?
@@crkphy sir, during selection of macromolecules when sir select native ligand so how to know which native lig. we select for docking with our ligand or drug molecule? 2. when we select native lig. it's means we select binding site for docking? 3. if it's really binding site then in PDB protein they already define binding area by attaching ligand we have to just remove their lig. & attached our own?
Hello, sir. Thank you for the tutorial. I have actually been using PyRx for over 3 years now. One thing that is bugging me recently is that, the binding energy is not reproducible. That means, the binding energy changes every time dock the same ligand with the same protein. I am using PyRx version 0.8 in windows 10 64-bit.
This same thing happened to every softwares like maestro schrodinger even autodock also.....i think its because of the conformational change of protein and ligand structures
Compare it with a reference ligand in case your target protein has one. And choose the best pose compared with the native dockd regarding ∆G Aka binding energy and low RMSD value. If you encounter close results, perform short Molecular dynamic ~10ns to differentiate which pose more stable inside the pocket.
Sir can we docked two target site for same disease by single ligand? Sir suppose x naam kaa ek ligand h jo A naam ke target site ko inhibit krra ho , phir suppose wahi x naam kaa ligand B naam ke target site ko inhibit krra ho, to sir kya hum ek saath A ligand ko dono target site(A and B) pe ek he saath docking kra skte h..... Multiple target site docking.... Sir plz doubt clear kar dijiye Agar kar sakte hain to kese ? Nahi kar sakte hain to kyu ni kr sakte?
Hello Sir, thank you so much for the video, it was really helpful. I have a question, the program only gives you the binding energy of the ligands, how can I look for the ki instead? Thank you.
Hello Sir, Thankyou for such an amazing video. But here I'm having two questions, I hope you'll answer them. 1. We have to select native ligands by own or do we have to do any literature survey for that? While doing blind docking we have to do native ligand procedure or just need to make grid box all over the protein structure? 2. This video is for blind docking or active site? Kindly answer. Thankyou.
I have the same doubt, sir. For my protein, I am not able to find any native ligand or active site. So, should I expand the grid all over the protein structure, sir?
Can you please post a vedio of docking and simulation of ionic liquids ( ionic compounds) to proteins or drug-ionic liquid docking . Taking ionic liquids ar solvent of target molecule and drug as ligand.
If I use with auto dock wizard, am not able to select the local ( autodock binary) which is at the bottom. Hence I cannot proceed after grid. Is there any way to select that
Hi sir, can you please tell how to find out the best ligand among the 3 ligands and how can we tell best docked ligand /pose one among the 10 results. Thank you
i use pyrx for docking, and use multiple ligands i download them from zinc database (nubben database for natural compounds), i do minimization and docking but when finish the result are encodede for the compound it just codded the energy , and they are 2332 compound how can i know the compound crosspend to each result???
Many thank for this video. each time tried to convert the protein to macromolecule but get this error message "list.remove(x): x not in list". How can I overcome this error. I have tried uninstalling and re-installing but not working
I would like to ask you how can we save the energy file lower rmsf upper rmsd all files together instead of individual saving I ask this because energy is one important criteria in screening. Thank you
basically i am chemistry person, but now i have some interest about this field. but i am totally new so, kindly tell me how enlarge the protein size. Thank you sir.
