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Molecular docking for Beginners in Hindi | Docking tutorial in Hindi | Basic Science Series Hindi

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Basic Science Series Hindi

Basic Science Series Hindi

Күн бұрын

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============================================
AutoDock Vina: vina.scripps.edu/
PyMOL: pymol.org/2/
PDB: www.rcsb.org/
Docking tutorials in window in Hindi,
How to do molecular docking tutorial in Hindi,
How to use Protein data bank in Hindi,
You need to install PyMOL in Hindi,
You need to install autodock took to follow the tutorial in Hindi,
How to do Protein receptor download in Hindi,
How to prepare protein (depends on protein to protein) in Hindi,
How to remove water molecule from protein structure in Hindi,
How to save the ligand from the ligand receptor complex in Hindi,
How to find coordinate information of ligand using grid box in Hindi,
How to use command prompt for docking in Hindi,
Make config.txt file in Hindi,
How to read the docking results in Hindi,
How to use autodock grid box in Hindi,
How to run vina.exe command in Hindi,
How to see docking poses of ligand in Hindi,
How to interpret docking results in Hindi,
Virtual screening of ligands on receptors in Hindi,
Reference:
[1] O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry 31 (2010) 455-461
[2] S. Forli, R. Huey, M. Pique, M. Sanner, D. Goodsell and A. Olson, "Computational protein-ligand docking and virtual drug screening with the AutoDock suite", Nature Protocols, vol. 11, no. 5, pp. 905-919, 2016. Available: 10.1038/nprot.2016.051.
Support my work at www.patreon.co...
Twitter: / drkumarlokender
Facebook: / lokenderkumar.sharma
Linkedin: / dr-lokender-kumar-5852...
Disclaimer: The information provided is for educational purposes only. We hold no responsibility for any issue, concerns, or damage arising from the content of our video.

Пікірлер: 220
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
Thank you for your kind Support. Please stay tuned. Thank you
@travelwithpaalii007
@travelwithpaalii007 8 ай бұрын
Bhupendra jogi sir 🙏🏼bohot acha explain kiya dil se 💓
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 12 күн бұрын
😅 thanks! I wish was that viral
@tanmayjana8796
@tanmayjana8796 3 жыл бұрын
Much needed video ♥️
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
Thank you very much! I am glad you liked it. If you have any questions please send me an email at luckysharma07@gmail.com, I will help with the trouble shooting. Stay tuned for more videos like this. Thanks you for your comment !!!
@abhishekkumar9011
@abhishekkumar9011 3 ай бұрын
After passing out shoolini uni, I learned how much someone can learn from you.
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi Ай бұрын
Thanks for your comment! Wishing you success 👍🏼🙏🏽
@aanchaltyagi9457
@aanchaltyagi9457 2 жыл бұрын
Sir, muje apki iss docking vdo se docking bhot acche se smj agya h so plz....MD simulation ka b ek vdo.....
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 2 жыл бұрын
Thanks for your support! I will try my best in future 🙏
@lifesciencedecoded
@lifesciencedecoded 3 жыл бұрын
As we all know that docking simply interaction between receptor and ligand molecule, before docking we do remove the water molecule and some other additional ligands molecule , and add polar hydrogen bond also, Afer that we dock between receptor and ligand molecules, and more negative sign give the good stability.....but sir my question is that in natural condition how water and additional ligands remove from receptor molecules and how will i add polar hydrogen also?
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
You can go as close as possible with interfering the system too much but you can’t simulate exactly the same condition in the system. This is the biggest limitation of the in silicon system. You so the best you can do. Try with water molecule and see what results you get. It will be good to see and compare. Let us know what you get ! 👏👌
@avantikaachari4747
@avantikaachari4747 28 күн бұрын
Sir one request : I am planning to buy new laptop for doing molecular docking for my final year project so pls suggest me some list of good affordable & durable laptops🙏🏻🙏🏻🙏🏻🙏🏻
@satviksharma9843
@satviksharma9843 3 жыл бұрын
Sir can you please make a video on what to do after doing b tech in biotechnology
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
Thank you for your valuable suggestion. I will try to make video on the topic you have suggested. Please stay tuned. Thank you for your valuable comment !
@miteshs5531
@miteshs5531 3 жыл бұрын
Apne bahut ache se explain kiya bhai
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
Thank you 🙏 brother for appreciating the video. I hope it was helpful.
@miteshs5531
@miteshs5531 3 жыл бұрын
Sir app ek antibody docking pe bhi ek video banayie
@manideepgoud7122
@manideepgoud7122 3 ай бұрын
Sir, can you make video on how to run hole2 programme for protein pore calculation
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi Ай бұрын
Okk will try
@LifeScienceswithJyothiSri
@LifeScienceswithJyothiSri 3 жыл бұрын
Informative sir tq
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
Thank you very much JyothiSrii for your valuable comment 🙏
@aanchaltyagi9457
@aanchaltyagi9457 2 жыл бұрын
Sir plz MD simulation ka bhi tutorial video upload kr dijiye for beginners with tools
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 2 жыл бұрын
Thanks for your support! I will try my best in future 🙏
@lifesciencedecoded
@lifesciencedecoded 2 ай бұрын
Sir which software is used to predict the anti-cancer compound ?
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi Ай бұрын
Well that might take combination of softwares
@chemistprojh4044
@chemistprojh4044 3 жыл бұрын
Great
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
Thanks a lot!!
@lifesciencedecoded
@lifesciencedecoded 3 жыл бұрын
Sir kya aap ucsf chimera main detailed video bana denge , its my humble request to you sir.... Av tak you tube main ucsf chimera main koi video nahi bani h....
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
I ll try dear. Thanks for your request
@zahidbashirzargar7564
@zahidbashirzargar7564 2 жыл бұрын
Thank you very much... Very helpful Sir...
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 2 жыл бұрын
Thank you for your feedback 🙏
@drpramodmahish6549
@drpramodmahish6549 2 жыл бұрын
Thank you for the interesting video, I am facing difficulty in the interpretation of result after docking of molecule to the protein.
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi Жыл бұрын
Thank you for your comment. Thank you for your support! I hope the video was helpful.
@shehlaakber5511
@shehlaakber5511 2 жыл бұрын
thank u so much , such a informative video
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 2 жыл бұрын
Glad it was helpful! Your appreciation is my motivation!
@ManishKumar-cr4ue
@ManishKumar-cr4ue 3 жыл бұрын
If possible then please make a demo on MD simulation by GROMACS or YASARA.. Anyway very informative video sir..
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
Thanks for your comment! I would love to make a video on that but I am using windows for this and GROMACS works on Linux systems. May be if I have set up in future I ll make video in the same. However I must say that from GROMACS tutorials are self explanatory. Imp part is how to analyze the trajectories. Stay tuned ! Thanks for the comment!
@DevendraTiwariPBB
@DevendraTiwariPBB 3 жыл бұрын
very helpful sir thank you
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
Thank you for your valuable comment 🙏
@swetanimwal7332
@swetanimwal7332 2 жыл бұрын
Thanku sir very helpfull video
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 2 жыл бұрын
Thank you for your comment!
@swetanimwal7332
@swetanimwal7332 2 жыл бұрын
Sir please help NS3 docking
@anshumansingh7598
@anshumansingh7598 2 жыл бұрын
Thank you
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 2 жыл бұрын
Thank you for your kind feedback
@artiverma7667
@artiverma7667 2 жыл бұрын
good morning sir i am arti verma , doing ph.D in ayurvedic pharmaceutical sciences in which I made madicne with mercury and sulphar ,combo of this is Hgs , so I want the knowledge how I can perform further things regarding molecular docking
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi Жыл бұрын
Great! Follow the tutorial and we will see how it works for you...
@Allaroundmhakal
@Allaroundmhakal Жыл бұрын
Thnanku
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 9 ай бұрын
Thank you
@dr.rameshkumar2386g
@dr.rameshkumar2386g 3 жыл бұрын
Very nicely explained.... Sir, could you please send the script for mol docking
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
Hi thanks for the comment. I am working to develop a course on the same and the script will be available with that. I will keep you notified. However if you follow the video you should be able to complete the process. Thank you 🙏
@aakashmourya1045
@aakashmourya1045 2 жыл бұрын
Thankyou so much sir
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 2 жыл бұрын
You are most welcome 🙏
@smartbaayoacademy4444
@smartbaayoacademy4444 3 жыл бұрын
Sir make video on molecular dynamics simulation
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
Good idea dear, I am dong MD simulations using HPC and not many people use HPC for MD simulations also GROMACS tutorial are self explannatory itself. Let me know if you need any help with MD simulations Thanks for posting your valuble comment!
@ushasingh9944
@ushasingh9944 2 жыл бұрын
Thank you sir
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 2 жыл бұрын
So nice of you
@thebiobuddy9595
@thebiobuddy9595 3 жыл бұрын
Thankyou so much
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
You're welcome 🙏 thanks for watching the video..
@mehreenkanwalchemistryteac4842
@mehreenkanwalchemistryteac4842 Жыл бұрын
Why different poses of ligand are obtain in docking process?
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 9 ай бұрын
Different affinity and sites
@mehreenkanwalchemistryteac4842
@mehreenkanwalchemistryteac4842 Жыл бұрын
Sir can I dock another different kind of ligand molecule on this protein receptor? In such way can we design the new structure formula of drug?
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 9 ай бұрын
You can but it may not show interactions
@lutfunchowdhury5711
@lutfunchowdhury5711 8 ай бұрын
THANK YOU SIR
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 12 күн бұрын
So nice of you
@intizaarmehdi1952
@intizaarmehdi1952 3 жыл бұрын
Thank you sir ❤️
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
You are welcome dear. Thank you.
@drganeshsmhaske1979
@drganeshsmhaske1979 3 жыл бұрын
Very informative video sir
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
Thank you Ganesh 🙏 I am thankful that you like my effort... your comment is really motivating...🙏🙏
@sharaddadhich9198
@sharaddadhich9198 2 жыл бұрын
How to dock with different ligand?? Can we use different ligand like any other molecule ethanol or isopropanol.
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 2 жыл бұрын
Sure you can get the pdb file of the ligand and dock it using the software
@sparksgaming2694
@sparksgaming2694 2 жыл бұрын
Sir please make video on gold suite 5.3
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 2 жыл бұрын
Thank you for your comment, I will try my best to make the same
@yashvashisht1805
@yashvashisht1805 Жыл бұрын
How to download auto dock and other software on Mac montrey ? I do not have access to windows or linux
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi Жыл бұрын
I suggest you use windows system but it is doable in Mac also.
@farzadmolani7435
@farzadmolani7435 Жыл бұрын
Thanks for the wonderful video. I've done docking for a series of GPCR with their native ligands using MOE. Unfortunately, the obtained affinity and rmsd aee not reproducible. I did as below: First I downloaded a pdb file. Removed all unwanted compounds and water molecules. In presence of the native ligand I did a quickprep. Finally docking (by default parameters). Could you please help me with my problem? By the way I saw in some video, some people do minimization before quickprep. Do you suggest it?
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi Жыл бұрын
Thank you! You can do that.
@JyotiBaliyan-pu5bk
@JyotiBaliyan-pu5bk 7 ай бұрын
Plzzz help in docking
@NikhilKumar-hk9nk
@NikhilKumar-hk9nk 2 жыл бұрын
Any journal which publishes results based on just molecular docking and not simulations
@nutribox4535
@nutribox4535 3 жыл бұрын
thank you make more
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
Thank you for your valuable comments and feedback 🙏
@adityagupta7510
@adityagupta7510 2 жыл бұрын
Sir Can I do it with none-protein molecule
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 2 жыл бұрын
This is only for protein molecule
@adityagupta7510
@adityagupta7510 2 жыл бұрын
@@BasicScienceSeriesHindi If we prepare the optimized files of our product..is there is any chances for doing it
@samardeepsinghrawat7026
@samardeepsinghrawat7026 2 жыл бұрын
Can we separate protein and Ligand through pimole and get their pdb I’d to dock them in hdock sir plz tell?
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 2 жыл бұрын
Yes you can..
@amitkarmakar1684
@amitkarmakar1684 3 жыл бұрын
Dear sir, please upload some demos of Metaboanalyst
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
Thank you for your feedback 🙏
@nilupandey8417
@nilupandey8417 2 жыл бұрын
Docking of PDB ID-5E7M and PDB ID 2NN2 ka result analysis ek bar show bata digeye
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 2 жыл бұрын
Thanks for your comments. Due to work load it won't be possible to run the exp but I can help with your project in the best possible way. What are these proteins and why you want to dock them?
@nilupandey8417
@nilupandey8417 2 жыл бұрын
@@BasicScienceSeriesHindi PDB ID 2NN2 Molecule-zBTB7A To determine the activity of anti cancerous compound which may work as effective anti cancerous drug for cure of cancer disease
@nilupandey8417
@nilupandey8417 2 жыл бұрын
Select cyproterone
@abhipshakhadanga8449
@abhipshakhadanga8449 2 жыл бұрын
@@nilupandey8417 hey were you able to do it ?
@nilupandey8417
@nilupandey8417 2 жыл бұрын
@@abhipshakhadanga8449 no
@abhipshakhadanga8449
@abhipshakhadanga8449 2 жыл бұрын
What tools or method we should use to inhibit a protein interacting to its receptor to supress the disease?
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 2 жыл бұрын
A ligand molecule is used for this. Thanks for your comment,
@shoaibrao8656
@shoaibrao8656 Жыл бұрын
sir i want your help for my thesis.....
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi Жыл бұрын
Thank you so much for your kind comment! What help you need?
@m.moaazanwar5270
@m.moaazanwar5270 Жыл бұрын
Sir I got the error "could not open "config.txt" for reading." when irun the command kindly help me out in that regard
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi Жыл бұрын
Do you have confix file in the folder?
@shahnawazahmadbhat3983
@shahnawazahmadbhat3983 Жыл бұрын
I am not able to get the text file of the x,Z centres file where you got it, sir
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi Жыл бұрын
You need to make it.
@shanmohy-ud-din9059
@shanmohy-ud-din9059 3 жыл бұрын
sir how you indentify which protein you can used for over leading compunds
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
Depending upon your research hypothesis you need to select a prptein. Are you working with a specific protein?
@swatishilwant2744
@swatishilwant2744 2 жыл бұрын
Can you please provide therotical material with aim or purpose of protein molecular docking?
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 2 жыл бұрын
Thank you for your feedback, I will try my best! Stay tuned!
@mehreenkanwalchemistryteac4842
@mehreenkanwalchemistryteac4842 Жыл бұрын
Docking only applicable to design the proteinious base drugs ?
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 9 ай бұрын
Majorly for proteins
@AyeshaKhan-rd7li
@AyeshaKhan-rd7li 6 ай бұрын
sir kia ap thesies work ma mry co supervisior bn skty han to plz content mee
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 4 ай бұрын
Your collage will have its own teachers they can be your superiors
@RAPSARO
@RAPSARO 2 жыл бұрын
Is it beneficial in master in pharmacology?
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 2 жыл бұрын
Sure! I what is your interest?
@lifesciencedecoded
@lifesciencedecoded 3 жыл бұрын
Sir can we docked two target site for same disease by single ligand? Sir suppose x naam kaa ek ligand h jo A naam ke target site ko inhibit krra ho , phir suppose wahi x naam kaa ligand B naam ke target site ko inhibit krra ho, to sir kya hum ek saath A ligand ko dono target site(A and B) pe ek he saath docking kra skte h..... Multiple target site docking.... Sir plz doubt clear kar dijiye Agar kar sakte hain to kese ? Nahi kar sakte hain to kyu ni kr sakte?
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
Any ligand can have multiple binding site. You can dock one ligand at two different sites. Compare there score, find interactions and that will tell you what is best site for the ligand. However you need to experimentally validate such results.
@lifesciencedecoded
@lifesciencedecoded 3 жыл бұрын
Thank you sir jii
@sumanGupta-vv5gu
@sumanGupta-vv5gu Жыл бұрын
Benefits of molecular docking sir??
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi Жыл бұрын
Thank you for your comment. It helps in lead compound identification.
@nancybhura5591
@nancybhura5591 3 жыл бұрын
Can you please show, how to measure h bonds, length between different residues and how to interpret the data from pymol for publications?
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
Thanks for your feedback! 🙏
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
To do so there are various methods you can use in pymol, I will try to covet the topic In near future. Please explore the pymol Wiki that will help you. Let me know if you any questions regarding the same. Thank you for your comment 🙏
@amulyadeshmanya6744
@amulyadeshmanya6744 Жыл бұрын
I am actually getting the error: could not open " protein.pdbqt" for reading in command prompt
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi Жыл бұрын
Plz follow the steps exactly as mentioned in the video.
@anamikasaini1196
@anamikasaini1196 2 жыл бұрын
Hlo sir...can you please tell how add parameters in autodock 4 ....because my ligand contain silicon.....it shows error that si is not of autodock type.......
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 2 жыл бұрын
What is the error? Paste your error here
@anamikasaini1196
@anamikasaini1196 2 жыл бұрын
@@BasicScienceSeriesHindi thank you sir for reply ....but the error is solved now 😅
@harshikakothari5423
@harshikakothari5423 3 жыл бұрын
At 12.12 mins, sir you told to save ligand How to save only ligand? For protein I selected atom n deleted the ligand
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
You need to save ligand as pdbqt file to complete be docking. This can be done using auto dock ligand tab. What errors are you getting ?
@harshikakothari5423
@harshikakothari5423 3 жыл бұрын
@@BasicScienceSeriesHindi ohh okay sir..thank you! I wanted to know if we can download ligand from pubchem
@akhilender3211
@akhilender3211 2 жыл бұрын
Sir how to do inhibitory molecule search for interleukin 2 cytokine
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 2 жыл бұрын
Nice project! Answer is not strain forward. If you are looking for insilico hits you can do virtual screening. But SPR technique with this protein would give you actual inhibitors.
@abhipshakhadanga8449
@abhipshakhadanga8449 2 жыл бұрын
@@BasicScienceSeriesHindi can you please make a video on virtual screening or drug discovery ?
@quantumworld9487
@quantumworld9487 10 ай бұрын
Sir how we download configuration file..yeah mujy smj nhi aara..plz help..baki sab smj gya hu
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 9 ай бұрын
Make a txt file just by right clicking...
@soumyasingh1624
@soumyasingh1624 Жыл бұрын
Hello sir i have obtained the output file and when i open both the output and receptor pdbqt file in pymol, they're too far away from each other, what are the possible causes for it and how do i rectify it?
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi Жыл бұрын
Redo it and recheck.
@lifesciencedecoded
@lifesciencedecoded 3 жыл бұрын
Sir suupose hum ek research article likh rahe hain , sir kya hum comparison ke liye aesa kar sakte hain kya, jese remdesivir ke liye dimension xyz alag rakh rahe hain isme humne docking autodock vina , command prompt waale step se docking ki , or other multiple ligands ke liye humne autodock vina , command prompt se docking nahi ki more than two ligands hone ke usse , isme humne pyrx virtual screening ka use kiya or dimension xyz bhi different rakhi as compare to remdesivir... To sir kya hum comparison kar sakte hain ab remdesivir or ye multiple ligands kaa.... Yaa hume sabhi ligands ke liye pyrx virtual screening he krni pdegi , agar hum research article m isko publish karana chahte hain to.... Sir koi problem create to nahi hogi dimension different rakhkr comparison kiya karkr
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
Select the top Ligands and do the docking with those ligand using auto doc with different exhaustiveness. This might support your conclusion. Thanks for your comment and hope the ans was helpful!
@lifesciencedecoded
@lifesciencedecoded 3 жыл бұрын
Tq sir
@draman23ization
@draman23ization 6 ай бұрын
Sir, Is educational version of pymol free lifetime?
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 4 ай бұрын
Yes
@shifaansari2491
@shifaansari2491 Жыл бұрын
SIR MAI M.PHARM KARRI HU SIR MUJHE MOLECULAR DOCKING PAR HI EK MAJOR PROJECT KARNA HAI TO PLEASE GUIDE ME KAISE START KARU PLEASE SIR
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi Жыл бұрын
Follow the video and see if you can understand this.
@abhisheknegi3478
@abhisheknegi3478 2 жыл бұрын
how to check where my ligand binding with the protein. kindly show that too
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 2 жыл бұрын
Thanks for your feedback. I ll try my best to make a video on that too.
@chemistprojh4044
@chemistprojh4044 3 жыл бұрын
DFT par video please sir
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
Thank you for your comment! I ll try to post videos on the same! Thanks
@lifesciencedecoded
@lifesciencedecoded 3 жыл бұрын
sir same dimensions rakhne main result alag alag kyu aata hai, jese maine ek ligand ke liye dimension x, y, z 30,40,50 rakhi or binding energy 10 aare h autodock vina se, but jab main yahi dimension rakhta hu same lifand ke liye, par is time main pyrx virtual screening tool se karta hu to result 9 binding energy kyu aata hai
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
The way the a programs work can provide you different output. It’s how they consider the parameters. You should email to authors and get exact information.
@lifesciencedecoded
@lifesciencedecoded 3 жыл бұрын
Sir mere binding energy pyrx virtual tool se -12.2kcal/mol aare h , but DSV se result analyse krne m unfavourable bumps, alkyl, vandevall interaction aese show hore hain.... To sir kya ye galat hai
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
If you are using Pyrx and following the standard protocol then you don’t have to worry. Read some literature, perform experiments in triplicate and if that is reproducible then you are good to go. Make sure you run control experiments. Don’t try different software, stick to one and you are good. Your binding energies are good. 👏👍
@lifesciencedecoded
@lifesciencedecoded 3 жыл бұрын
@@BasicScienceSeriesHindi Thank you so much sir
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
@@lifesciencedecoded My pleasure!
@abdulashikkhan5912
@abdulashikkhan5912 3 жыл бұрын
Metal ion or nanoparticles ka docking kaise kare, please make video on it
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
Thank you for your kind feedback 🙏
@lifesciencedecoded
@lifesciencedecoded 3 жыл бұрын
Is there any rule regarding which chain should be kept and which one should be deleted ?
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
If they are same you can use any chain. It depends on what you want to test? For e.g. binding pockets etc.
@lifesciencedecoded
@lifesciencedecoded 3 жыл бұрын
Thanku sir , sir aapke pass time ho to ek video bnaye is par aap
@DevendraTiwariPBB
@DevendraTiwariPBB 3 жыл бұрын
please make video NAMD and VMD in hindi
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
Thank you for your feedback!
@lifesciencedecoded
@lifesciencedecoded 3 жыл бұрын
Cyp 17 ko pyrx virtual screen tool main upload karne se alternate conformation bata raha hai, or pdbqt file main convert nahi ho raha hai....
@lifesciencedecoded
@lifesciencedecoded 3 жыл бұрын
Kese convert kare sir
@lifesciencedecoded
@lifesciencedecoded 3 жыл бұрын
Sir ye grid set kese karte hain, means inme x,y,z center kis base par rakhte h....
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
Thank you for your comment and feedback. Grid box set kerne k Bahut sare reasons ho sakte hain Jaise ligand binding site, full structure ye depend karega what you are trying to do ? It is related to the scientific hypothesis. Can you explain your project I might be able to help other wise it would be confusing for you. Thanks
@lifesciencedecoded
@lifesciencedecoded 3 жыл бұрын
Actually sir main practicer hu av , main soch raha tha ki how to set the box of grid....
@lifesciencedecoded
@lifesciencedecoded 3 жыл бұрын
Ek video multiple ligand docking pyrx m bna dijiye
@sunilsethi3465
@sunilsethi3465 3 жыл бұрын
Thank you sir. Much helpful But sir i am facing an issue while doing the command prompt. Can u plz help me out.. 🙏
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
What’s the issue ?
@sunilsethi3465
@sunilsethi3465 3 жыл бұрын
@@BasicScienceSeriesHindi sir, while writing command for the config file.. "Config conf.txt". It is showing that ' The file can't be opened for reading'. What to do next.. i 've tried several times..
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
@@sunilsethi3465 I can say anything for sure. Make sure the file name matched with command line. It should be the same. Are you familiar with Linux commands ?
@sunilsethi3465
@sunilsethi3465 3 жыл бұрын
@@BasicScienceSeriesHindi No sir, i am not familiar with linux. No idea at all about that.. But thank you so much sir. Finally the results came. I did it. Waiting for lot more such vdos like that. Thank you 🙏🙏🙏
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
@@sunilsethi3465 Glad to hear! Great.
@mominzarinamdnajeeb8269
@mominzarinamdnajeeb8269 3 жыл бұрын
Most expected
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
🙏🙏🙏
@chemistprojh4044
@chemistprojh4044 3 жыл бұрын
Computational methods I want to learn and software for free version
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
Thank you for your comment! I ll try to post related videos in future!
@dikeshraipur7290
@dikeshraipur7290 Жыл бұрын
Sir iska best results jo ata h docking ka usko results ko word me kese likhenege kya ap help krenge sir
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi Жыл бұрын
Make a table of the results.
@MohmadRafeeqLone
@MohmadRafeeqLone 2 жыл бұрын
Sir please can give me the script regarding the steps of commands
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 2 жыл бұрын
Thanks for your comment, I am designing a course on the same. Stay tuned and will share the updates.
@satishchem8651
@satishchem8651 2 жыл бұрын
Hi, Sir good morning. I am Satish, I saw your video its very interesting and helpful for me. I am a chemistry research scholar, my field is origin and evolution of life, in which I synthesize biomolecules like amino acids, peptides, nucleic acid base in prebiotic conditions. Like Miller and Urey experiment and surface interaction study of these biomolecules on prebiotically available clay like montmorillonite clay. so can you suggest me how can I dock a biomolecules on montmorillonite clay, or is it possible or not for docking processes.
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 2 жыл бұрын
Thanks for your comment, Autodock vina is only used protein and ligand docking
@RAPSARO
@RAPSARO 2 жыл бұрын
Sir can u suggest me laptop model in which I can apply docking n software name
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 2 жыл бұрын
You can do docking on any decent system. Don’t go for very expensive or specific model.
@RAPSARO
@RAPSARO 2 жыл бұрын
@@BasicScienceSeriesHindi thanks sir
@RAPSARO
@RAPSARO 2 жыл бұрын
@@BasicScienceSeriesHindi sir can we research a new molecular identity drugs by using those software sir I m master in pharmacology student can I search any new drugs or molecular research through my studies-???
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 2 жыл бұрын
@@RAPSARO Yes you can. You can do virtual docking experiments using the compounds available in ZINC data base and identify the new activity of these compounds, This is one way to do research. Finally these must be tested in the lab. What disease you are focusing on?
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 2 жыл бұрын
@@RAPSARO Sure! My pleasure. Thank you for your comments!
@ankitkeshariya317
@ankitkeshariya317 Жыл бұрын
Hlw sir can you please provide me your script of this video
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi Жыл бұрын
I am working on making the course on this. Please follow the steps in the video for now. Thanks!
@shanzamunir7506
@shanzamunir7506 3 жыл бұрын
Please answer Config file humny khud bnani hoti h?
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
Yes. Make a txt file.
@shanzamunir7506
@shanzamunir7506 3 жыл бұрын
@@BasicScienceSeriesHindi Thanks I am Facing another problem during command, can you help me out with this?
@nandu6489
@nandu6489 12 күн бұрын
Sir o jo Blue or red box aya hi nhi na
@sararehman5715
@sararehman5715 Ай бұрын
I am not able to get config file
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi Ай бұрын
Please follow the steps and create the file as .txt file
@rushikeshgarade9390
@rushikeshgarade9390 3 жыл бұрын
I tried to save my file as .pdbqt but it gets save as PyMol.pdbqt in extension.. can anybody help??
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
Are you naming it correctly ? I seems like your extension is right ! Can you open the file in vina ?
@rushikeshgarade9390
@rushikeshgarade9390 3 жыл бұрын
@@BasicScienceSeriesHindi while i type codes in vina it is not working
@aakashmourya1045
@aakashmourya1045 2 жыл бұрын
Please provide me receipt
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 2 жыл бұрын
I am in process of designing the course for the same. This might take time. Stay tuned ! Thanks
@pharmacywidmuskan
@pharmacywidmuskan 3 жыл бұрын
Extra precision docking.... ???
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 3 жыл бұрын
Thanks for your comment!
@madhusudan7335
@madhusudan7335 Жыл бұрын
Good morning Sir...plz provide your Email to get script
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi Жыл бұрын
I working on the making the course so please till now watch the entire video. it helps the channel to grow. thanks .
@ankitkeshariya317
@ankitkeshariya317 Жыл бұрын
I didn’t recognise your mail id
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi Жыл бұрын
Description of many videos have the links for various social media platform.
@rajkumarsahoo3337
@rajkumarsahoo3337 2 жыл бұрын
Sir, please give me your email id. I want the script of this molecular docking.
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi 2 жыл бұрын
Thank you for contacting, I will be designing a course on this and make the same available to all, stay tuned and I will share the details
@shoaibrao8656
@shoaibrao8656 Жыл бұрын
sir kindly tell me your mail id please
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi Жыл бұрын
Thank you so much for your kind comment! Check the description box.
@ignitedmind7703
@ignitedmind7703 Жыл бұрын
Thank you so much sir ❤️
@BasicScienceSeriesHindi
@BasicScienceSeriesHindi Жыл бұрын
So nice of you
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