Sir plz give one lecture about Pharmacophor based modeling. Sir your lecture is so informative.
@Prof.Dr.MuhammadNaveed3 жыл бұрын
sure and noted
@leoking30683 жыл бұрын
Sir! Please discuss some rules or methods that should be followed during PROTEIN-DNA docking and standard parameters.
@Prof.Dr.MuhammadNaveed3 жыл бұрын
sure and mostly discussed in PyMol lecture
@Okibur7 ай бұрын
why that server giving this message "You don't have permission to access this resource" isn't that free?
@OmKumar-wm4kb Жыл бұрын
thankyou sir..👍
@botanylectures343411 ай бұрын
sir if we made a novel compound, how can we get its structure for molecular docking
@muazfaruque8520 Жыл бұрын
Respected Sir, Can you please make a tutorial on advanced option with active receptor site,.........
@fatimanoor54243 жыл бұрын
Boht.. Aala .. Sir...
@Prof.Dr.MuhammadNaveed3 жыл бұрын
welcome dear
@studywithamisha9903 Жыл бұрын
How to do metal dependent protein docking and simulation plz make vdo on that
@user-pj6wq6fm4m3 жыл бұрын
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
@Prof.Dr.MuhammadNaveed3 жыл бұрын
use PyMol or this tool www.bonvinlab.org/pdb-tools/
@shbangash4373 жыл бұрын
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
@Prof.Dr.MuhammadNaveed3 жыл бұрын
use PyMol or watch my lecture on it
@ramneetkaur25003 жыл бұрын
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,
@Prof.Dr.MuhammadNaveed3 жыл бұрын
better both on PDB but can covert file into pdb
@ramneetkaur25003 жыл бұрын
@@Prof.Dr.MuhammadNaveed Thanks Dr. Naveed. I have converted them into pdb files. Again you are doing a great job.
@sakibhossen002 жыл бұрын
Dear sir, after downloading the docked file from patchdock or cluspro, how can I visualise the interaction between two proteins???
@ramneetkaur25003 жыл бұрын
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?
@Prof.Dr.MuhammadNaveed3 жыл бұрын
top listed model and ACE value then further PyMol highlights interaction
@ramneetkaur25003 жыл бұрын
@@Prof.Dr.MuhammadNaveed Thanks Dr. Naveed for your help.
@shanmohy-ud-din90593 жыл бұрын
Aoa, how ican identify which protein are used my leading compound
@Prof.Dr.MuhammadNaveed3 жыл бұрын
literature
@nilanjanaghosh82882 жыл бұрын
Thankyou so much Sir for this discussion.
@Prof.Dr.MuhammadNaveed2 жыл бұрын
Glad to hear that
@fernandacuevas71293 жыл бұрын
Hi. A have a question: what is ACE measured in? Thanks
@Prof.Dr.MuhammadNaveed3 жыл бұрын
it is Atomic contact energy between two molecules
@sajandas38043 жыл бұрын
Plz suggest me the best figure name of ion and small molecules you identified
@Prof.Dr.MuhammadNaveed3 жыл бұрын
dear do with anyone
@KHANADARIWithAmmaG2 жыл бұрын
Assalamualaikum sir Kya ap plz CDOCKER k baray main Kuch bta sakty hain ?
@Prof.Dr.MuhammadNaveed2 жыл бұрын
sure
@ahmadnaveed1703 жыл бұрын
Sir what mean software citation.
@Prof.Dr.MuhammadNaveed3 жыл бұрын
means how to cite this tool in your article
@sabahatjavid86422 жыл бұрын
I want to learn docking how I learn?
@nimrahzafar51883 жыл бұрын
Well done & really appreciate ur work... But sir kindly help me out ligand ligand interaction can be performed??
@Prof.Dr.MuhammadNaveed3 жыл бұрын
yup use batch dock
@SufyanKhan-qv4js2 жыл бұрын
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.MuhammadNaveed2 жыл бұрын
waslam yes can do or use cluspro
@SufyanKhan-qv4js2 жыл бұрын
@@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
@bhagatsingh63453 жыл бұрын
Nice lacturer sir❤️
@Prof.Dr.MuhammadNaveed3 жыл бұрын
welcome dear
@duafatima62832 жыл бұрын
Hi Dr. Naveed! How can we show these results in our thesis, via screenshots?
@Prof.Dr.MuhammadNaveed2 жыл бұрын
better to use the download or copy option
@muhammadabraryousaf10623 жыл бұрын
Sir, do we need to prepare the protein (removal of water, the addition of hydrogen, charge etc.) before uploading?
@Prof.Dr.MuhammadNaveed3 жыл бұрын
no you can do with out this
@likhithamallela5553 жыл бұрын
Sir what is the drug and the protein you used
@safiadaultana45903 жыл бұрын
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
@Prof.Dr.MuhammadNaveed3 жыл бұрын
yes can be
@safiadaultana45903 жыл бұрын
@@Prof.Dr.MuhammadNaveed Jaza kallah Khair
@MuzzammelRehman3 жыл бұрын
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)
@lifesciencedecoded3 жыл бұрын
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.....
@Prof.Dr.MuhammadNaveed3 жыл бұрын
watch results interpretation and interactions my PyMol
@princeroyal65033 жыл бұрын
Sir! Which docking tool is best autodock vina or patch dock for drug designing?
@Prof.Dr.MuhammadNaveed3 жыл бұрын
autodock vina
@sanaanwer79603 жыл бұрын
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?
@Prof.Dr.MuhammadNaveed3 жыл бұрын
yes can do but check at PyMol
@rabbiamalik9966 Жыл бұрын
sir binding energy ksy calculate hngi isii tool ko use kr k
@zubairsharifmuhammadsharif34333 жыл бұрын
Sir if file is large then how can I perform protein ligand interaction profiler?
@Prof.Dr.MuhammadNaveed3 жыл бұрын
then use PyMol
@bhagatsingh63453 жыл бұрын
Sir siRNA kaise design kre...is pe next lacturer dijiyega sir.
@Prof.Dr.MuhammadNaveed3 жыл бұрын
dear noted but first to finish docking series then sure will share
@jyotibala1023 жыл бұрын
Why PATCH DOCK score show positive and negative ACE values with so.much drastic change
@Prof.Dr.MuhammadNaveed3 жыл бұрын
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
@jyotibala1023 жыл бұрын
@@Prof.Dr.MuhammadNaveed thankyou, so we should consider high score and Ace in minus for the preferences. ACE is related energy or ???
@Prof.Dr.MuhammadNaveed3 жыл бұрын
@@jyotibala102 Yes dear highest score and lowest ACE energy
@jyotibala1023 жыл бұрын
Thanks Dr Naveed. I appreciate your efforts and knowledge sharing on public domain.
@lola-mn2kw3 жыл бұрын
Sir.is there is english version from this video?
@Prof.Dr.MuhammadNaveed3 жыл бұрын
will share soon
@samarpitadash63143 жыл бұрын
Sir how to download protein and ligand both from pdb database
@Prof.Dr.MuhammadNaveed3 жыл бұрын
download complex
@dr.rimshariaz46883 жыл бұрын
Sir plz upload tutorial for FirDock also
@Prof.Dr.MuhammadNaveed3 жыл бұрын
its most part same as PatchDock but noted
@namalkhan69563 жыл бұрын
Sir I am not getting results by same method of patch dock