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.
Really appreciate this channel. It's an immense pleasure to see bioinformatics flourishing in Pakistan. Thank you, sir! looking forward to more great videos.
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 ?
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
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.
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.
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
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 .
first identify plant reported as medicinal importance against diabetics then check plant metabolite alkaloid flavonoid and enzyme role in treatment of this disease
@@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 .
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.
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
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
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
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.
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
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
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
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 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?
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
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
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
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
This lecture was excellent ❤❤❤ I really need this type of video for my thesis work. Thank you sir 😊😊
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.
This is indeed an excellent explanation, especially, Sir, you have given description of every term and phenomena. Appreciated!
welcome dear
Thank You sir for Wonderful explanation... recently got know abt Ur channel n m sure this channel is blessing for Bioinformatics Students 😊
In sha Allah
Aditya from India, Great Video Dr Naveed
thanks, dear and pleasures
Thank you soo much sir .. your lecture is too much helpfull and easy to understand
Sir , your teaching method is so amazing. I hope you will be fine and accept my heartiest greetings.
welcome dear
Thank you so much sir,for better explanation about docking
welcome dear
It’s so kind of you sir. Your lectures help me a lot.
jazakAllah
Really appreciate this channel. It's an immense pleasure to see bioinformatics flourishing in Pakistan. Thank you, sir! looking forward to more great videos.
Pleasures
This is very helpful and excellent explanation..thanks alot
Very helpful, easy to understand. but afsos is baaat pe h k pihle q nahi dekhe ye videos...... anyway, thank you so much sir
.
pleasures dear
thank you for such an informative lecture. Sir
Waiting for the next part
Sure very soon
Great Work.
Thankyou so much sir!! Have been waiting for so long. Highly appreciated
Thanks alot
@@Prof.Dr.MuhammadNaveed sir can you please elaborate the main basic concept for medicinal plants that have potential drugs for diabetic
@@kkkhooptongs5599 best way to confirm this is only from the literature on ethnobotany articles
You are doing great work...
glads it helps you
Thankyou so much sir!! Have been waiting for so long
So nice of you
Very informative..God bless you
Kindly make videos on insilico vaccine designing
InshaAllah very soon the docking video will be uploaded. This procedure also can be used for vaccine designing.
Thank u
informative as always and see right on time :D
Thankyou
Very Informative Lecture..
pleasures
Very informatic .thank u sir
Pleasures and welcome dear
Sir, secondary metabolites ki molecular docking .. protein ligand (autodock vina) se hi hogi??
yes can do
Thank you so much Sir for superb tutorial..!
welcome
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 ?
try to run again or use some other tool for docking then do compare
thanks from India
love from Pakistan
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
nothing then go for docking if prepared
Thank u sir
AOA sir.. Kindly answer that what is '' exhaustiveness'' in conf file?... Please answer sir
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.
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.
And I have clearly 1st part of docking.
I am excited for coming 2nd part.
ruclips.net/video/9emli0xf4O0/видео.html
Dear sir, I need help in dynamic programing, block game , alogrithem design for this
We only work on Bioinformatics and Molecular Biology.
i need your help, I am working on RASMOL , Pymol and discovery studio. Can i write an article by using these softwares of bioinformatics.
you can compare it but at the level of stat and programing
@@Prof.Dr.MuhammadNaveed Thanku Sir
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
do paste yourself vina in C folder
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 .
first identify plant reported as medicinal importance against diabetics then check plant metabolite alkaloid flavonoid and enzyme role in treatment of this disease
@@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 .
@@kkkhooptongs5599 you can drop your queries through email and my teaching assistant will reach u shortly as possible.
aqibmirza67@gmail.com
@@Prof.Dr.MuhammadNaveed certainly Sir
Very helpful video, thanks. Just I want to know what are the methods used for in silico vaccine design rather than docking ?
Sure very soon
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.
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
Dear Dr. Kindly include a slide in the end of steps involved in your lecture
Good suggestion and try to add in the next lectures
why do we need a grid box for ligand before docking? Plz ans sir
this cover the protein active site where can find interaction among protein and ligand
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
Is there any software which can help in ligand ligand docking instead of protein ligand docking sir
Dear sir is there any global platform where i can get certication in these software and digital programs .kindly provide some information
no need of it just learn all and apply in research
God bless you more sir :)
Ameen thanks dear
Thank you so much sir for your explanation. Sir kindly send links of the protein-ligand docking research paper. Thank you.
just write this keyword on google and find many articles
Sir how can we know which ligand we should use?
Very well explained sir from India 🤗🤗🤗🤗🤗🤗🤗
Welcome dear pleasures
Thank you so much sir
welcome dear
Could u plz tell me how to give citations and referneces in our paper?
ruclips.net/video/lFUM3M_oYok/видео.html
Thank u so much
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
you can do with any protein and any ligand and its not depend upon I-TASER
Sir can you please suggest a book for practical bioinformatics, please sir
essential Bioinformatics by Xiong
Sir can you plz tell me about the importance of this like in energy determination or in others also
We can find the affinity of the interacting molecules
sir plzz help me to choose a suitable protein and a ligand
Sir india main best CADD course (medium hindi + english language = hinglish) kon se institute se kare plz guide kijiyega....
try to do from english institute
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
can do easily by following my lectures
Sir , discovery studio download nhi ho rha hai, license mang rha h
Kya kre sir??
download from here. www.3dsbiovia.com/products/collaborative-science/biovia-discovery-studio/visualization-download.php
My protein is not available in desired organism at PDB what should i do
design by chemdraw or pymol
sir can you explain why we prefer lowest binding energies?
its show close or tight binding
what arethe ligands that we can use for docking
its might be a drug or protein or any chemical which can be download from drugbank
Sir mere pas new version hn tu ye old version kese download karen
Sir how we can choose the proper receptor to have interaction with our ligind
randomly or form literature
Well! God bless you.
Ameen and Pleasures
sir can you please send the link of your slides!
dear you can follow these slide or just download this video
Sir kindly make video on comparative genome analysis
Sure. Very soon.
Sir g MGL tool 32bit windows ka liya ha 64 ka liya nhi ha... What i should do then
64
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.
this can do here but use PYMOL
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
Bht accha sir
pleasures
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
Yes use HADDOCK for this regard
Dr. Muhammad Naveed ok professor thank you so much
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
@@ihsanullah8140 yes possible these complexes can interact as a ligand
Anyone have link or tutorial how to download auto dock vina?
Link is mentioned at the start of this video
Yes sir
AOA sir! MD simulation pe notes or koi b handouts Hai tu kindly share kr dyn
plz make a video downloadable sir
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
you do first check from literature and if not found then do share here compound names here
@@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?
@@meenumaurya3995 docking is possible on every molecule but its results decided whether docking good or bad according to literature comparison
@@Prof.Dr.MuhammadNaveed okay sir
.....thanks alot...but sir mujhe docking me apki help chahie ......aap help kar denge meri?
Thank you sir.
Most welcome
In silico immunesimulation par ik videos bnadoo please sir
noted
Salam sir may I know are you from Karachi?
waslam, from Lahore
log text ke andar kya likhna hai sir
Already mentioned script in video
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
Noted dear but docking also written same in native language anyhow will share lecture in english soon
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
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
To check the sensitivity and resistivity of antibiotic with the phytochemicals present in my plant by docking
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
yes can take it
yup
sir protein protein intrction kaise predict karnge.
use STRING
@@Prof.Dr.MuhammadNaveed thank you so much sir
Sir please protein protein docking ka kuch batay
Sure dear very soon
Asalam ul akuim Dr shb
Waslam
Ap itni door bth k q lecture dty hain
means ?
Sir pymol pe video banao please
Done and today will share
@@Prof.Dr.MuhammadNaveed thanku so much....😊😊😊🥰
@@Prof.Dr.MuhammadNaveed sir ,ek bar fasta sequence alignment par bhi full video banao. And multiple sequence alignment par bhi
Sab log ap ki hi video dekhna chahte h ,mere frii
Sir Apne normally multiple sequence alignment par, clustal w Ka example deke video banaya h
👍
Sir chimera ka bta de plzzz😔😔
will share lecture on it
Kundan