Molecular Docking Overview | Protein-Ligand Docking | Lecture 10 Part 1 | Dr. Muhammad Naveed

[@Chemistano]

This lecture was excellent ❤❤❤ I really need this type of video for my thesis work. Thank you sir 😊😊

[@unboxing4u766]

very informative Dr. Saheb ! I am from synthetic chemistry background with little information in this field but keen to know a lot in this area. Just started and looking for every related videos in this area.

[@feelingless-is-meaningless4654]

This is indeed an excellent explanation, especially, Sir, you have given description of every term and phenomena. Appreciated!

[@Prof.Dr.MuhammadNaveed]

welcome dear

[@235aditya]

Aditya from India, Great Video Dr Naveed

[@Prof.Dr.MuhammadNaveed]

thanks, dear and pleasures

[@gm1567]

Thank You sir for Wonderful explanation... recently got know abt Ur channel n m sure this channel is blessing for Bioinformatics Students 😊

[@Prof.Dr.MuhammadNaveed]

In sha Allah

[@faridasiddika4773]

It’s so kind of you sir. Your lectures help me a lot.

[@Prof.Dr.MuhammadNaveed]

jazakAllah

[@hirasana3135]

Kindly make videos on insilico vaccine designing

[@Prof.Dr.MuhammadNaveed]

InshaAllah very soon the docking video will be uploaded. This procedure also can be used for vaccine designing.

[@hirasana3135]

Thank u

[@hasnainbaqir1072]

Sir , your teaching method is so amazing. I hope you will be fine and accept my heartiest greetings.

[@Prof.Dr.MuhammadNaveed]

welcome dear

[@shahzainab5443]

Thank you soo much sir .. your lecture is too much helpfull and easy to understand

[@Error-uu6nr]

Sir, secondary metabolites ki molecular docking .. protein ligand (autodock vina) se hi hogi??

[@Prof.Dr.MuhammadNaveed]

yes can do

[@Gautamkumar-om7im]

Thank you so much sir,for better explanation about docking

[@Prof.Dr.MuhammadNaveed]

welcome dear

[@sabahafeez6503]

Thankyou so much sir!! Have been waiting for so long. Highly appreciated

[@Prof.Dr.MuhammadNaveed]

Thanks alot

[@kkkhooptongs5599]

@@Prof.Dr.MuhammadNaveed sir can you please elaborate the main basic concept for medicinal plants that have potential drugs for diabetic

[@Prof.Dr.MuhammadNaveed]

@@kkkhooptongs5599 best way to confirm this is only from the literature on ethnobotany articles

[@kkkhooptongs5599]

Sir ..how do we select the protein and ligand for plants that possess potential drugs for diabetics ..please elaborate th very main basic concept for a beginner like me... And I got the interest watching your youtube channel ..thanking you .

[@Prof.Dr.MuhammadNaveed]

first identify plant reported as medicinal importance against diabetics then check plant metabolite alkaloid flavonoid and enzyme role in treatment of this disease

[@kkkhooptongs5599]

@@Prof.Dr.MuhammadNaveed thank you sir ..indeed respect you with ur instant reply .a great teacher like you will surely change many lives .. Sir ,a personal request from you ...do you provide your contact details for future queries, otherwise these are my contact details Mail-bawngmei@gmail 9774277517 what's app no. With due regard and may God bless you in your future endeavours. K.thang India .

[@Prof.Dr.MuhammadNaveed]

@@kkkhooptongs5599 you can drop your queries through email and my teaching assistant will reach u shortly as possible. [e-mail]

[@kkkhooptongs5599]

@@Prof.Dr.MuhammadNaveed certainly Sir

[@toobanadeem3595]

Really appreciate this channel. It's an immense pleasure to see bioinformatics flourishing in Pakistan. Thank you, sir! looking forward to more great videos.

[@Prof.Dr.MuhammadNaveed]

Pleasures

[@yaswanthrao6489]

Sir Greetings I have a doubt.is it required to docking for a standard compound.suppose I am doing on compounds related to anti diabetic should I compare binding energy with acarbose

[@biology.lectures351]

thank you for such an informative lecture. Sir Waiting for the next part

[@Prof.Dr.MuhammadNaveed]

Sure very soon

[@qazinajamwajiwaji216]

This is very helpful and excellent explanation..thanks alot

[@Hzjsjekksns]

Very informative..God bless you

[@jahangirahmed9335]

Sir I have prepared ligand liberary in discovery studio then after what are the basic step to pre process these ligand ready for docking and check errors

[@Prof.Dr.MuhammadNaveed]

nothing then go for docking if prepared

[@jahangirahmed9335]

Thank u sir

[@noorrana2164]

Great Work.

[@manojdhameja4212]

Sir, i had performed molecular docking of a standard inhibitor against a target enzyme. Both Vina and Autodock were used (active site docking). Vina results are good and are same as present in literature, but Autodock results are very different with wrong binding affinity. Why is it so ? With vina, inhibitor is binding to active site however with Autodock inhibitor is not binding to active site and goes to anywhere else. What to do now ?

[@Prof.Dr.MuhammadNaveed]

try to run again or use some other tool for docking then do compare

[@AnmolSingh-nq2jr]

thanks from India

[@Prof.Dr.MuhammadNaveed]

love from Pakistan

[@ihassanabidi]

Very Informative Lecture..

[@Prof.Dr.MuhammadNaveed]

pleasures

[@MuhammadAfzal-st2ls]

You are doing great work...

[@Prof.Dr.MuhammadNaveed]

glads it helps you

[@MuhammadHassan-qj7do]

Very helpful, easy to understand. but afsos is baaat pe h k pihle q nahi dekhe ye videos...... anyway, thank you so much sir .

[@Prof.Dr.MuhammadNaveed]

pleasures dear

[@azrashabir2606]

Sir mere pas new version hn tu ye old version kese download karen

[@AliRaza-hc9fn]

Thankyou so much sir!! Have been waiting for so long

[@Prof.Dr.MuhammadNaveed]

So nice of you

[@laibarajput3878]

AOA sir.. Kindly answer that what is '' exhaustiveness'' in conf file?... Please answer sir

[@Prof.Dr.MuhammadNaveed]

Vina has a parameter called “exhaustiveness” that controls how comprehensive its search is. The more the exhaustiveness, the less the probability a good result is missed.

[@mriganka7331]

Very helpful video, thanks. Just I want to know what are the methods used for in silico vaccine design rather than docking ?

[@Prof.Dr.MuhammadNaveed]

Sure very soon

[@sheryar3418]

why do we need a grid box for ligand before docking? Plz ans sir

[@Prof.Dr.MuhammadNaveed]

this cover the protein active site where can find interaction among protein and ligand

[@geetanjalisaini4989]

Is there any software which can help in ligand ligand docking instead of protein ligand docking sir

[@ajaymanaithiya5014]

Thank u sir, for teaching about docking I am M. Pharma students from pharmaceutical chemistry department. I want to learn docking. How do docking. So i am waiting part 2 docking to learn.

[@ajaymanaithiya5014]

And I have clearly 1st part of docking. I am excited for coming 2nd part.

[@Prof.Dr.MuhammadNaveed]

kzbin.info/www/bejne/b5bQnZxmrctnhZI

[@juniorkidscorner]

Sir how can we know which ligand we should use?

[@virendratiwari407]

Sir ji mujhe in-silico study me Ph.D k work karni hai jo ki Anti diabetic drug se related hai meri physalis Peruviana and solanum nigrum spicies hai molecular docking molecular dynamics karni hai

[@Prof.Dr.MuhammadNaveed]

can do easily by following my lectures

[@hasnainbaqir1072]

i need your help, I am working on RASMOL , Pymol and discovery studio. Can i write an article by using these softwares of bioinformatics.

[@Prof.Dr.MuhammadNaveed]

you can compare it but at the level of stat and programing

[@hasnainbaqir1072]

@@Prof.Dr.MuhammadNaveed Thanku Sir

[@muhammadnaumanchaudhry6446]

Dear sir, I need help in dynamic programing, block game , alogrithem design for this

[@Prof.Dr.MuhammadNaveed]

We only work on Bioinformatics and Molecular Biology.

[@affiafifa6766]

Very informatic .thank u sir

[@Prof.Dr.MuhammadNaveed]

Pleasures and welcome dear

[@yasmeenfazikazi4092]

Dear Dr. Kindly include a slide in the end of steps involved in your lecture

[@Prof.Dr.MuhammadNaveed]

Good suggestion and try to add in the next lectures

[@muddasirkhan7904]

Hello sir, I have installed all the app on your provided link but in final step i have didn't find the vina folder in my C: drive due to which the commond prompt not run kindly guide me thanks

[@Prof.Dr.MuhammadNaveed]

do paste yourself vina in C folder

[@iqrasajid1679]

Thank you so much Sir for superb tutorial..!

[@Prof.Dr.MuhammadNaveed]

welcome

[@sobiarani2542]

Could u plz tell me how to give citations and referneces in our paper?

[@Prof.Dr.MuhammadNaveed]

kzbin.info/www/bejne/one4fmaDlNSMpc0

[@sobiarani2542]

Thank u so much

[@laibamir5021]

sir plzz help me to choose a suitable protein and a ligand

[@lifesciencedecoded]

Sir india main best CADD course (medium hindi + english language = hinglish) kon se institute se kare plz guide kijiyega....

[@Prof.Dr.MuhammadNaveed]

try to do from english institute

[@syedbukhari1124]

informative as always and see right on time :D

[@Prof.Dr.MuhammadNaveed]

Thankyou

[@safbilal]

Dear sir is there any global platform where i can get certication in these software and digital programs .kindly provide some information

[@Prof.Dr.MuhammadNaveed]

no need of it just learn all and apply in research

[@zunairafaiz2729]

Sir g MGL tool 32bit windows ka liya ha 64 ka liya nhi ha... What i should do then

[@Prof.Dr.MuhammadNaveed]

64

[@saadbinayub8280]

God bless you more sir :)

[@Prof.Dr.MuhammadNaveed]

Ameen thanks dear

[@ajitmaurya3226]

Sir , discovery studio download nhi ho rha hai, license mang rha h Kya kre sir??

[@Prof.Dr.MuhammadNaveed]

download from here. www.3dsbiovia.com/products/collaborative-science/biovia-discovery-studio/visualization-download.php

[@kailashbhandari6703]

Thank you so much sir for your explanation. Sir kindly send links of the protein-ligand docking research paper. Thank you.

[@Prof.Dr.MuhammadNaveed]

just write this keyword on google and find many articles

[@ihsanullah8140]

Mera ph.d ka research topic hai synthesis of metal complexes and their DNA binding activity dr shb kia mian docking DNA aur metal complexes ka laya use kar skta ho g

[@Prof.Dr.MuhammadNaveed]

Yes use HADDOCK for this regard

[@ihsanullah8140]

Dr. Muhammad Naveed ok professor thank you so much

[@ihsanullah8140]

Dr. Muhammad Naveed Dr shb main main pora metal complex ko DNA k sath docking krna chachta ho srf ligand nahi mery kam copper aur zinc complexes pr hai g

[@Prof.Dr.MuhammadNaveed]

@@ihsanullah8140 yes possible these complexes can interact as a ligand

[@insia3910]

Very well explained sir from India 🤗🤗🤗🤗🤗🤗🤗

[@Prof.Dr.MuhammadNaveed]

Welcome dear pleasures

[@vishalbeldar1716]

Thank you for the Easy steps of docking. But when I follow these steps in the command prompt there is error occurred 'could not open "cont.txt" for reading' How to overcome such type of errors.

[@Prof.Dr.MuhammadNaveed]

Thanks, dear and you are doing one mistake put conf file in C drive rather than on desktop then give the command. Hopefully it works

[@chitrasharma2427]

Sir can you plz tell me about the importance of this like in energy determination or in others also

[@Prof.Dr.MuhammadNaveed]

We can find the affinity of the interacting molecules

[@zarbabkhan4799]

Sir.... how to perform Molecular Docking when results are obtained from I-Tasser Tool. There is a confusions that which Ligand are to be selected for interaction in the process. Kindly help. thanks

[@Prof.Dr.MuhammadNaveed]

you can do with any protein and any ligand and its not depend upon I-TASER

[@sanjaisrao484]

Sir can you please suggest a book for practical bioinformatics, please sir

[@Prof.Dr.MuhammadNaveed]

essential Bioinformatics by Xiong

[@zunairafaiz2729]

My protein is not available in desired organism at PDB what should i do

[@Prof.Dr.MuhammadNaveed]

design by chemdraw or pymol

[@MayankSingh-uj6hi]

Bht accha sir

[@Prof.Dr.MuhammadNaveed]

pleasures

[@ushasingh9944]

Thank you so much sir

[@Prof.Dr.MuhammadNaveed]

welcome dear

[@meenumaurya3995]

Hello sir, ....I am working on project related to docking, but mujhe y nhi pta ki uska docking possible Hoga ya nhi....kya aap MERI help Kar sakte h?...plz aap apna no. De sakte h , MERI BHT help hogi mere project ko Pura Karne m

[@Prof.Dr.MuhammadNaveed]

you do first check from literature and if not found then do share here compound names here

[@meenumaurya3995]

@@Prof.Dr.MuhammadNaveed I search literature but do hi paper mile usse related.....actually mera jo project h uska title hai molecular docking studies about action of beta blockers on SARS COV-2...... Isi p mujhe docking karni hai ....actually jo paper mila usme theoretical h or ek mila jisme docking to h beta blocker par effective nhi.....to mujhe yhi janna h ki ispe docking hogi ya nhi?

[@Prof.Dr.MuhammadNaveed]

@@meenumaurya3995 docking is possible on every molecule but its results decided whether docking good or bad according to literature comparison

[@meenumaurya3995]

@@Prof.Dr.MuhammadNaveed okay sir .....thanks alot...but sir mujhe docking me apki help chahie ......aap help kar denge meri?

[@NedaMAlam]

sir can you explain why we prefer lowest binding energies?

[@Prof.Dr.MuhammadNaveed]

its show close or tight binding

[@biryani6861]

Sir how we can choose the proper receptor to have interaction with our ligind

[@Prof.Dr.MuhammadNaveed]

randomly or form literature

[@azqaawanblogs4003]

what arethe ligands that we can use for docking

[@Prof.Dr.MuhammadNaveed]

its might be a drug or protein or any chemical which can be download from drugbank

[@architsaxena8342]

log text ke andar kya likhna hai sir

[@Prof.Dr.MuhammadNaveed]

Already mentioned script in video

[@muhammmadzainriaz4572]

sir can you please send the link of your slides!

[@Prof.Dr.MuhammadNaveed]

dear you can follow these slide or just download this video

[@indraneeldhavale5683]

Anyone have link or tutorial how to download auto dock vina?

[@Prof.Dr.MuhammadNaveed]

Link is mentioned at the start of this video

[@aqsachaudhary1969]

A.o.a Sir ligand apny kha koi b phytochemicals ya drug ho gy and jo target h wo koi b protein ya enzyme ho ga lkn agr mai ny kisi antibiotic ki sensitivity check krni h ya resistivity or mai antibiotic ko as a ligand lon gy lkn jo meray phytochemicals h mere plants mai jo present h to mai phr usko as a target lon gy kindly clear this point pls

[@aqsachaudhary1969]

And Sir jo strains ya pathogens mai use kr rhi hoon wo to nhi ad ho gy is ki interaction check krni k liye just antibiotics and phytochemicals use ho gy bs

[@aqsachaudhary1969]

To check the sensitivity and resistivity of antibiotic with the phytochemicals present in my plant by docking

[@aqsachaudhary1969]

Sir hum antibiotic ko as a protein ly gy and phytochemicals present in our plant usko as a ligand ly gy? Lkn jin pathogens k against mai ye sarey kuch check kr rhi thee us ko b ad kry gy docking mai interaction check krni k liye agr kry gy ad to kaisy kry gy Sir

[@Prof.Dr.MuhammadNaveed]

yes can take it

[@Prof.Dr.MuhammadNaveed]

yup

[@aqsamuzaffar1927]

Sir kindly make video on comparative genome analysis

[@Prof.Dr.MuhammadNaveed]

Sure. Very soon.

[@nilamlalwani6327]

Yes sir

[@prof.syedrizwanabbas]

Well! God bless you.

[@Prof.Dr.MuhammadNaveed]

Ameen and Pleasures

[@tubakhan2518]

A.O.A Sir, can you please guide how to use two co-receptor CCR5 and CXCR4 as protein for dual antagonist such as NF279 or any other derivative in molecular docking. I want to see how one molecule attaches to two co-receptors. Please sir can you provide any email address for student query.

[@Prof.Dr.MuhammadNaveed]

this can do here but use PYMOL

[@MuzzammelRehman]

for this use protein-protein docking by Cluspro , HADDock or patchdock etc then use any visualiser to see how they are connected you can also use online server

[@artwithamar]

plz make a video downloadable sir

[@mariamrana5264]

AOA sir! MD simulation pe notes or koi b handouts Hai tu kindly share kr dyn

[@zahoorahmad2711]

In silico immunesimulation par ik videos bnadoo please sir

[@Prof.Dr.MuhammadNaveed]

noted

[@bhagatsingh6345]

sir protein protein intrction kaise predict karnge.

[@Prof.Dr.MuhammadNaveed]

use STRING

[@bhagatsingh6345]

@@Prof.Dr.MuhammadNaveed thank you so much sir

[@mahparafaraz1609]

Salam sir may I know are you from Karachi?

[@Prof.Dr.MuhammadNaveed]

waslam, from Lahore

[@rehanulhaque4523]

Thank you sir.

[@Prof.Dr.MuhammadNaveed]

Most welcome

[@ihsanullah8140]

Asalam ul akuim Dr shb

[@Prof.Dr.MuhammadNaveed]

Waslam

[@misbahhayat7178]

Ap itni door bth k q lecture dty hain

[@Prof.Dr.MuhammadNaveed]

means ?

[@mohammedahmedjalloh531]

Next time indicate you will be lecturing in your native language in the title, so that we dont have to waste the 5 seconds to watch your pictures and wait for the lecture to start. thanks

[@Prof.Dr.MuhammadNaveed]

Noted dear but docking also written same in native language anyhow will share lecture in english soon

[@MayankSingh-uj6hi]

Sir please protein protein docking ka kuch batay

[@Prof.Dr.MuhammadNaveed]

Sure dear very soon

[@maheshswami5226]

Sir pymol pe video banao please

[@Prof.Dr.MuhammadNaveed]

Done and today will share

[@maheshswami5226]

@@Prof.Dr.MuhammadNaveed thanku so much....😊😊😊🥰

[@maheshswami5226]

@@Prof.Dr.MuhammadNaveed sir ,ek bar fasta sequence alignment par bhi full video banao. And multiple sequence alignment par bhi

[@maheshswami5226]

Sab log ap ki hi video dekhna chahte h ,mere frii

[@maheshswami5226]

Sir Apne normally multiple sequence alignment par, clustal w Ka example deke video banaya h

[@nain9038]

Sir chimera ka bta de plzzz😔😔

[@Prof.Dr.MuhammadNaveed]

will share lecture on it

[@kirankhan6568]

👍

[@kundankumarsingh3141]

Kundan