Asalam Alekum Sir yeah pdb mein Jo ribbon structure format kaisey design kartey Hain kindly iska mujhey is ka software aur tareeqa bataein. . thanks in advance sir
Hello Dr. Naveed. Your lectures are great and I really like them. I am trying to use Patch dock to do docking between a protein and a chemical from a natural product( curcumin from turmeric). Should both structures be present in the protein data bank. Can you please help me with this. Many Thanks. Best Regards,
Dr, Naveed, What does the value of the score tell us in the patch dock results. What is the significance of the score in terms of the interaction between ligand and protein?
AOA sir how are you? Sir, can I use patchdock to dock my model protein Omicron S protein with my macromolecule ligand 2S albumin, and my model flocculating protein ligand?
@@Prof.Dr.MuhammadNaveed ok thank you. Sir, can you tell me how because everytime I upload my protein as receptor molecule and my 2s albumin and model flocculating protein as my ligand molecule it sometimes gives me a message that as you uploaded an empty ligand or receptor molecule or sometimes sends me an error message via email. Can you help me to solve this issue? Thank you
ASSALAM.O.ALAIKUM! RESPECTED SIR Can we use this PLIP( Protein ligand interaction profiler) for Protein protein interaction to know that which ions and amino acids are involved for docking
There is no Option in PLIP for protein-protein interaction. It shows protein-peptide, DNA/RNA interactions. In this tutorial the interaction which has been showed by Dr Naveed are irrelevant because the docking was between the protein not with Ca+2 or Acetic acid ( for which the interactions has been shown in this video)
Thanku sir , first time maine docking ki with the help of patch dock, credit goes to you sir , aapki video se hi sikha..... Sir but result ko kese analysis kare ye samaj nahi aa raha hai , plz help me sir.....
Sir mai aik complex means transcription factor e2f1 and protein pRB k complex ko dock DNA k sath krwana chahti hon to kya mai same yehi method apply krn ge?
the positive score depends upon molecule size and surface interaction region but on the other hand ACE output of binding affinities of those interactions in negative values
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Sir plz give one lecture about Pharmacophor based modeling.
Sir your lecture is so informative.
sure and noted
Sir! Please discuss some rules or methods that should be followed during PROTEIN-DNA docking and standard parameters.
sure and mostly discussed in PyMol lecture
why that server giving this message "You don't have permission to access this resource" isn't that free?
thankyou sir..👍
sir if we made a novel compound, how can we get its structure for molecular docking
Respected Sir,
Can you please make a tutorial on advanced option with active receptor site,.........
Boht.. Aala .. Sir...
welcome dear
How to do metal dependent protein docking and simulation plz make vdo on that
I want to delete some chain from my pdb file.. but I can't identify the chain in that tools. Can you pls help me
use PyMol or this tool www.bonvinlab.org/pdb-tools/
Asalam Alekum Sir yeah pdb mein Jo ribbon structure format kaisey design kartey Hain kindly iska mujhey is ka software aur tareeqa bataein. . thanks in advance sir
use PyMol or watch my lecture on it
Hello Dr. Naveed. Your lectures are great and I really like them. I am trying to use Patch dock to do docking between a protein and a chemical from a natural product( curcumin from turmeric). Should both structures be present in the protein data bank. Can you please help me with this. Many Thanks. Best Regards,
better both on PDB but can covert file into pdb
@@Prof.Dr.MuhammadNaveed Thanks Dr. Naveed. I have converted them into pdb files. Again you are doing a great job.
Dear sir, after downloading the docked file from patchdock or cluspro, how can I visualise the interaction between two proteins???
Dr, Naveed, What does the value of the score tell us in the patch dock results. What is the significance of the score in terms of the interaction between ligand and protein?
top listed model and ACE value then further PyMol highlights interaction
@@Prof.Dr.MuhammadNaveed Thanks Dr. Naveed for your help.
Aoa, how ican identify which protein are used my leading compound
literature
Thankyou so much Sir for this discussion.
Glad to hear that
Hi. A have a question: what is ACE measured in? Thanks
it is Atomic contact energy between two molecules
Plz suggest me the best figure name of ion and small molecules you identified
dear do with anyone
Assalamualaikum sir Kya ap plz CDOCKER k baray main Kuch bta sakty hain ?
sure
Sir what mean software citation.
means how to cite this tool in your article
I want to learn docking how I learn?
Well done & really appreciate ur work... But sir kindly help me out ligand ligand interaction can be performed??
yup use batch dock
AOA sir how are you? Sir, can I use patchdock to dock my model protein Omicron S protein with my macromolecule ligand 2S albumin, and my model flocculating protein ligand?
waslam yes can do or use cluspro
@@Prof.Dr.MuhammadNaveed ok thank you. Sir, can you tell me how because everytime I upload my protein as receptor molecule and my 2s albumin and model flocculating protein as my ligand molecule it sometimes gives me a message that as you uploaded an empty ligand or receptor molecule or sometimes sends me an error message via email. Can you help me to solve this issue? Thank you
Nice lacturer sir❤️
welcome dear
Hi Dr. Naveed! How can we show these results in our thesis, via screenshots?
better to use the download or copy option
Sir, do we need to prepare the protein (removal of water, the addition of hydrogen, charge etc.) before uploading?
no you can do with out this
Sir what is the drug and the protein you used
ASSALAM.O.ALAIKUM! RESPECTED SIR
Can we use this PLIP( Protein ligand interaction profiler) for Protein protein interaction to know that which ions and amino acids are involved for docking
yes can be
@@Prof.Dr.MuhammadNaveed Jaza kallah Khair
There is no Option in PLIP for protein-protein interaction. It shows protein-peptide, DNA/RNA interactions. In this tutorial the interaction which has been showed by Dr Naveed are irrelevant because the docking was between the protein not with Ca+2 or Acetic acid ( for which the interactions has been shown in this video)
Thanku sir , first time maine docking ki with the help of patch dock, credit goes to you sir , aapki video se hi sikha..... Sir but result ko kese analysis kare ye samaj nahi aa raha hai , plz help me sir.....
watch results interpretation and interactions my PyMol
Sir! Which docking tool is best autodock vina or patch dock for drug designing?
autodock vina
Sir mai aik complex means transcription factor e2f1 and protein pRB k complex ko dock DNA k sath krwana chahti hon to kya mai same yehi method apply krn ge?
yes can do but check at PyMol
sir binding energy ksy calculate hngi isii tool ko use kr k
Sir if file is large then how can I perform protein ligand interaction profiler?
then use PyMol
Sir siRNA kaise design kre...is pe next lacturer dijiyega sir.
dear noted but first to finish docking series then sure will share
Why PATCH DOCK score show positive and negative ACE values with so.much drastic change
the positive score depends upon molecule size and surface interaction region but on the other hand ACE output of binding affinities of those interactions in negative values
@@Prof.Dr.MuhammadNaveed thankyou, so we should consider high score and Ace in minus for the preferences. ACE is related energy or ???
@@jyotibala102 Yes dear highest score and lowest ACE energy
Thanks Dr Naveed. I appreciate your efforts and knowledge sharing on public domain.
Sir.is there is english version from this video?
will share soon
Sir how to download protein and ligand both from pdb database
download complex
Sir plz upload tutorial for FirDock also
its most part same as PatchDock but noted
Sir I am not getting results by same method of patch dock
y? check your protein should be of single chain
Not getting results in email
@@namalkhan6956 check spasm folder
I have checked thousands time
I have checked thousands time
ye to work hi nahi kar raha hai😑
working
I thought he spoke English.
I thought he spoke English.