PatchDock | Molecular Docking of Enzymes with Drugs & Inhibitors | Lecture 26 | Dr. Muhammad Naveed

[@chokaravines2569]

Sir plz give one lecture about Pharmacophor based modeling. Sir your lecture is so informative.

[@Prof.Dr.MuhammadNaveed]

sure and noted

[@leoking3068]

Sir! Please discuss some rules or methods that should be followed during PROTEIN-DNA docking and standard parameters.

[@Prof.Dr.MuhammadNaveed]

sure and mostly discussed in PyMol lecture

[@Okibur]

why that server giving this message "You don't have permission to access this resource" isn't that free?

[@OmKumar-wm4kb]

thankyou sir..👍

[@botanylectures3434]

sir if we made a novel compound, how can we get its structure for molecular docking

[@muazfaruque8520]

Respected Sir, Can you please make a tutorial on advanced option with active receptor site,.........

[@fatimanoor5424]

Boht.. Aala .. Sir...

[@Prof.Dr.MuhammadNaveed]

welcome dear

[@studywithamisha9903]

How to do metal dependent protein docking and simulation plz make vdo on that

[@user-pj6wq6fm4m]

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.MuhammadNaveed]

use PyMol or this tool www.bonvinlab.org/pdb-tools/

[@shbangash437]

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.MuhammadNaveed]

use PyMol or watch my lecture on it

[@ramneetkaur2500]

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.MuhammadNaveed]

better both on PDB but can covert file into pdb

[@ramneetkaur2500]

@@Prof.Dr.MuhammadNaveed Thanks Dr. Naveed. I have converted them into pdb files. Again you are doing a great job.

[@sakibhossen00]

Dear sir, after downloading the docked file from patchdock or cluspro, how can I visualise the interaction between two proteins???

[@ramneetkaur2500]

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.MuhammadNaveed]

top listed model and ACE value then further PyMol highlights interaction

[@ramneetkaur2500]

@@Prof.Dr.MuhammadNaveed Thanks Dr. Naveed for your help.

[@shanmohy-ud-din9059]

Aoa, how ican identify which protein are used my leading compound

[@Prof.Dr.MuhammadNaveed]

literature

[@nilanjanaghosh8288]

Thankyou so much Sir for this discussion.

[@Prof.Dr.MuhammadNaveed]

Glad to hear that

[@fernandacuevas7129]

Hi. A have a question: what is ACE measured in? Thanks

[@Prof.Dr.MuhammadNaveed]

it is Atomic contact energy between two molecules

[@sajandas3804]

Plz suggest me the best figure name of ion and small molecules you identified

[@Prof.Dr.MuhammadNaveed]

dear do with anyone

[@KHANADARIWithAmmaG]

Assalamualaikum sir Kya ap plz CDOCKER k baray main Kuch bta sakty hain ?

[@Prof.Dr.MuhammadNaveed]

sure

[@ahmadnaveed170]

Sir what mean software citation.

[@Prof.Dr.MuhammadNaveed]

means how to cite this tool in your article

[@sabahatjavid8642]

I want to learn docking how I learn?

[@nimrahzafar5188]

Well done & really appreciate ur work... But sir kindly help me out ligand ligand interaction can be performed??

[@Prof.Dr.MuhammadNaveed]

yup use batch dock

[@SufyanKhan-qv4js]

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]

waslam yes can do or use cluspro

[@SufyanKhan-qv4js]

@@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

[@bhagatsingh6345]

Nice lacturer sir❤️

[@Prof.Dr.MuhammadNaveed]

welcome dear

[@duafatima6283]

Hi Dr. Naveed! How can we show these results in our thesis, via screenshots?

[@Prof.Dr.MuhammadNaveed]

better to use the download or copy option

[@muhammadabraryousaf1062]

Sir, do we need to prepare the protein (removal of water, the addition of hydrogen, charge etc.) before uploading?

[@Prof.Dr.MuhammadNaveed]

no you can do with out this

[@likhithamallela555]

Sir what is the drug and the protein you used

[@safiadaultana4590]

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.MuhammadNaveed]

yes can be

[@safiadaultana4590]

@@Prof.Dr.MuhammadNaveed Jaza kallah Khair

[@MuzzammelRehman]

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)

[@lifesciencedecoded]

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.MuhammadNaveed]

watch results interpretation and interactions my PyMol

[@princeroyal6503]

Sir! Which docking tool is best autodock vina or patch dock for drug designing?

[@Prof.Dr.MuhammadNaveed]

autodock vina

[@sanaanwer7960]

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.MuhammadNaveed]

yes can do but check at PyMol

[@rabbiamalik9966]

sir binding energy ksy calculate hngi isii tool ko use kr k

[@zubairsharifmuhammadsharif3433]

Sir if file is large then how can I perform protein ligand interaction profiler?

[@Prof.Dr.MuhammadNaveed]

then use PyMol

[@bhagatsingh6345]

Sir siRNA kaise design kre...is pe next lacturer dijiyega sir.

[@Prof.Dr.MuhammadNaveed]

dear noted but first to finish docking series then sure will share

[@jyotibala102]

Why PATCH DOCK score show positive and negative ACE values with so.much drastic change

[@Prof.Dr.MuhammadNaveed]

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

[@jyotibala102]

@@Prof.Dr.MuhammadNaveed thankyou, so we should consider high score and Ace in minus for the preferences. ACE is related energy or ???

[@Prof.Dr.MuhammadNaveed]

@@jyotibala102 Yes dear highest score and lowest ACE energy

[@jyotibala102]

Thanks Dr Naveed. I appreciate your efforts and knowledge sharing on public domain.

[@lola-mn2kw]

Sir.is there is english version from this video?

[@Prof.Dr.MuhammadNaveed]

will share soon

[@samarpitadash6314]

Sir how to download protein and ligand both from pdb database

[@Prof.Dr.MuhammadNaveed]

download complex

[@dr.rimshariaz4688]

Sir plz upload tutorial for FirDock also

[@Prof.Dr.MuhammadNaveed]

its most part same as PatchDock but noted

[@namalkhan6956]

Sir I am not getting results by same method of patch dock

[@Prof.Dr.MuhammadNaveed]

y? check your protein should be of single chain

[@namalkhan6956]

Not getting results in email

[@Prof.Dr.MuhammadNaveed]

@@namalkhan6956 check spasm folder

[@namalkhan6956]

I have checked thousands time

[@namalkhan6956]

I have checked thousands time

[@blossomCotton-y6k]

ye to work hi nahi kar raha hai😑

[@Prof.Dr.MuhammadNaveed]

working

[@1p53gen]

I thought he spoke English.

[@1p53gen]

I thought he spoke English.