10 ай бұрын
3 жыл бұрын
3 жыл бұрын
3 жыл бұрын
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Пікірлер
@tzewei0187 8 күн бұрын
Thank you for the tutorial. I have a question: if the ligand I want doesn’t have a 3D conformer in PubChem, what should I do?
@AKBIT 8 күн бұрын
You must convert to a 3D structure using a conversion tool.
@AKBIT 8 күн бұрын
Watch this video tutorial kzbin.info/www/bejne/j37IoWaFgNFkr80
@AKBIT 8 күн бұрын
Use CACTUS tool cactus.nci.nih.gov/translate
@tzewei0187 7 күн бұрын
Thank you very much!!!
@ahmetharunciftci 8 күн бұрын
Didnt understand anything at all👎🏻
@AKBIT 8 күн бұрын
First learn the algorithm basics
@ahmetharunciftci 7 күн бұрын
@@AKBIT I have just learned the local alignment score. In the video, you didnt explain it clearly. I had to look elsewhere to find out.
@AKBIT 7 күн бұрын
😄
@rukentanis6813 9 күн бұрын
I still dont get it man😭😭
@AKBIT 9 күн бұрын
Practice makes a man perfect 💪
@muralidharpandey6074 17 күн бұрын
Is it not possible in windows versions?
@AKBIT 16 күн бұрын
It is especially for Windows
@muralidharpandey6074 16 күн бұрын
@@AKBIT but I am not getting the result. Please give a video link in which permission related error can be resolved
@AKBIT 15 күн бұрын
To run the program as an administrator, right-click on the app to show the pop-down menu. Now click on 'Run as administrator', and the app will run as administrator.
@muralidharpandey6074 15 күн бұрын
@@AKBIT thank you sir By your guidance I have resolved the permission related problems but when I submit the job firstly the Gauss view opens and the job still runs 2 hours there were no any results and when I close the Gauss view the job also stops without any results
@AKBIT 15 күн бұрын
Test with a simple docking to check whether it is working.
@muralidharpandey6074 17 күн бұрын
When I am doing docking after final submission it gives error permission denied
@AKBIT 16 күн бұрын
You must grant administrative privileges to the software for storing results to the directory.
@muralidharpandey6074 15 күн бұрын
Please guide me for such a test dock
@AKBIT 15 күн бұрын
Follow the tutorial
@muralidharpandey6074 15 күн бұрын
@@AKBIT link please
@nurizzatizakaria871 Ай бұрын
Sir, how can I convert the rna to dna in pdb file?
@AKBIT Ай бұрын
It is not possible to convert RNA to DNA in a PDB file (for 3D coordinates). Instead you can convert RNA to DNA 🧬 sequence and then generate a 3D structure.
@Anosh_Saleem Ай бұрын
Very well done
@AKBIT Ай бұрын
Thank you for your feedback 🙂
@luismarioibarra2735 2 ай бұрын
Thank you for your tutorial, I just have one question, when I open the ligand file it automatically fits into the receptor, what could that mean?
@AKBIT Ай бұрын
It is your perspective with the viewer. If you zoom in, you can find the difference. The ligand places the screen according to the atomic co-ordinates in the file.
@dontshitamigo1260 2 ай бұрын
Thankyou so much for completing the half work being shown all over the youtube, almost all of the tutorial video stops at analysing the docked file, but not showing how to save the complex file for molecular dynamics.
@AKBIT Ай бұрын
You're very welcome!
@MotivationAtNeed 3 ай бұрын
SIR Could you kindly make a tutorial to deploy a custom BLAST Database from a server for a selected number of organisms, I want users to submit a sequence which can checked and results to be displayed. Thank You sir
@AKBIT 2 ай бұрын
Great suggestion! Kindly brief your query to my email [email protected]
@iqrahasan9114 3 ай бұрын
Good evening sir I have a query regarding autodock vina installation
@AKBIT 3 ай бұрын
What is your query?
@iqrahasan9114 3 ай бұрын
@@AKBITAutodock vina is not working properly on my laptop... Structure are not visible on the screen
@AKBIT 3 ай бұрын
AutoDock Vina is a command-line tool. I think you are using Python Molecular Viewer (PMV) for AutoDockTools (ADT).
@AKBIT 3 ай бұрын
If you have trouble in visualisation, check the GPU of your laptop.
@iqrahasan9114 3 ай бұрын
@@AKBIT but discovery studio is working & pymol also only autodock vina face this problem
@kshitijmohan6987 3 ай бұрын
If you don't have coding experience or a powerful computer you can use QuandleLabs to run Autodock Vina and perform docking
@Olcool 3 ай бұрын
Also since my Uni prot sequences are 2, and my teplate is one, but i should produce a model with the two units together, how do i submit the sequence fasta file?
@Olcool 3 ай бұрын
Hello. If i know the template that i need to use where should i place the template because in my case i am using 2 sequences (T1R1/T1R3) from Uniprot and a template (PDB ID: 1EWK) from protein databank.
@AKBIT 3 ай бұрын
You must choose interactive mode molecular modelling for multiple target sequence and custom template structure uploads. swissmodel.expasy.org/interactive#structure
@thedaytodaygirl 4 ай бұрын
Thanks a lot ❤❤❤❤
@AKBIT 4 ай бұрын
My pleasure ☺️
@Vikky5414 4 ай бұрын
How many days did it take
@AKBIT 4 ай бұрын
It is just like a molecular visualisation tool.
@Vikky5414 4 ай бұрын
@@AKBIT yes sir iam also a biotech student iam talking about the time it took to simulate
@Vikky5414 4 ай бұрын
@@AKBIT yes sir iam also a biotech student iam talking about the time it took to simulate
@AKBIT 4 ай бұрын
Actually I have downloaded the molecular dynamics trajectories file from the database for the visualisation. Usually MD simulation time depends on the molecule size, movement and system configuration.
@AKBIT 4 ай бұрын
Watch this video tutorial for explanation kzbin.info/www/bejne/o2eVnZpsj66hd6s
@verdant1723 4 ай бұрын
ty bro
@AKBIT 4 ай бұрын
My pleasure 😊
@professorswenson3504 4 ай бұрын
I do not see autodock vina as an option under tools and binding analysis. I downloaded autodock vina, but not sure how I get it to load into chimeraX
@AKBIT 4 ай бұрын
Are you using Chimera or ChimeraX?
@professorswenson3504 4 ай бұрын
@@AKBIT You are right, I was using ChimeraX. I am now trying to use PyRx for docking with ChimeraX, but it doesn't recognize my cxs file to open it.
@AKBIT 4 ай бұрын
ChimeraX does not have an interface to AutoDock Vina program. UCSF Chimera and UCSF ChimeraX are two different programs; you would need to get Chimera to use this feature.
@AKBIT 4 ай бұрын
If you are trying to use PyRx with AutoDock Vina, watch this video tutorial kzbin.info/www/bejne/fGiQY6FueNGVbJo
@FizzaJawad-zx7ye 4 ай бұрын
thank you soooo much this video helped me a lotttttttt
@AKBIT 4 ай бұрын
Thank you for your valuable feedback 😊
@choirocky 5 ай бұрын
It is very useful!
@AKBIT 5 ай бұрын
Thank you for the valuable feedback.
@aldeansyfr 5 ай бұрын
Thakyouu sir🙏🏻
@bnratha 6 ай бұрын
Can we make a homo-multimer or hetero-multimer of proteins in chimerax?
@wp1300 6 ай бұрын
0:44
@AKBIT 6 ай бұрын
!?
@naghmehsaba6890 6 ай бұрын
from amino acid sequenced to 3D structure via homology modeling option of chimera
@AKBIT 6 ай бұрын
Absolutely. Through the Modeller software.
@c.sahanareddy916 7 ай бұрын
Can we predict the novel derivatives of a compound using this application
@AKBIT 7 ай бұрын
Yes. But, based on the database availability.
@MariaRodriguez-nq8ys 7 ай бұрын
Pero si sale todo borroso el video!
@AKBIT 7 ай бұрын
Could you translate in English?
@bhanubanerjee23 8 ай бұрын
Thank you for the tutorial
@AKBIT 8 ай бұрын
You’re welcome 😊
@shiwanaLS 8 ай бұрын
sir can you tell me which is the best software tool currently for protein data analysis?
@AKBIT 8 ай бұрын
UCSF ChimeraX is the best alternative free software.
@MichaelAyenero 9 ай бұрын
so concise and enriching full of information. Thank you.
@AKBIT 9 ай бұрын
Thanks for your feedback 🙂
@marcela4189 9 ай бұрын
how do you change the color of the dots on the Van de Waals model?
@AKBIT 9 ай бұрын
It is not possible to customize dots color.
@AdnanAslamOfficial 10 ай бұрын
Please speak about what you are trying to show. It would be helpful for novices!!
@AKBIT 10 ай бұрын
Thanks for your feedback.
@hasankachal11 11 ай бұрын
Unfortunatly non of the websites working right now :(
@AKBIT 11 ай бұрын
Currently researchers are focusing on artificial intelligence to improve accuracy in structure prediction. So, most of the servers using old methods are deprecated or discontinued their services.
@anupdholam1113 Жыл бұрын
I could not find dimensions responsive 😟
@AKBIT Жыл бұрын
Press 'Ctrl + Shift + I' to show 'Dimensions' menu at top of the page. Select 'Responsive' from the list box. kzbin.info/www/bejne/a3yyfWmhj5WKaNksi=dcwDIUu7ygk6Xrjq&t=33
@verdant1723 4 ай бұрын
click elements
@tallatnaz Жыл бұрын
i wish you could explain this in Hindi as well.....
@AKBIT Жыл бұрын
Sorry, l don't know Hindi 😉
@nohataha6398 Жыл бұрын
when using blast for unknown it gives 75 similarity in identity of un known 16 r rna gene from bacteria ?? What is that mean 🤔
@AKBIT Жыл бұрын
FYI: The exact matching of characters in both sequences is known as identity. For example, APPLE = APPLE Furthermore, the partial matching of characters in both sequences is known as similarity. For example, APPLE ~ MAPLE
@SudhaMerla Жыл бұрын
What are Gasteiger and Kollman charges? Where exactly are these charges being added in the protein? How can I determine the location of these charges in the protein
@AKBIT Жыл бұрын
What are Gasteiger and Kollman charges? Refer: expertcomputationalchemistry.blogspot.com/2016/08/the-difference-between-kollman-charges.html Where exactly are these charges being added in the protein? Refer page 5: www.csb.yale.edu/userguides/graphics/mgltools/UsingAutoDockWithADT.pdf How can I determine the location of these charges in the protein? Compare the protein before and after adding charges to find the difference. It will be present in the PDBQT file.
@arunvijay4361 Жыл бұрын
Sir teach how to use bioedit software.
@AKBIT Жыл бұрын
Yes, sure. I'll post soon.
@arunvijay4361 Жыл бұрын
Thanks sir
@PabithraPN Жыл бұрын
Nice
@akanksharout5366 Жыл бұрын
Very nice sir Needed advice sir. Im new to this field how do I get my grip in bioinformatics.
@AKBIT Жыл бұрын
First you have to learn the basics of bioinformatics (theory aspect). Later, try simple practical like database, sequence alignment, molecule visualization, etc. After you are familiar, try molecular modeling, drug designing, docking, etc. If you are interested, you can also learn programming languages simultaneously or later. You must go on step-by-step.
@akanksharout5366 Жыл бұрын
@@AKBIT Thanks 🙏🏽 a ton Sir for responding... Please guide as to how to deepen the theory??? And which languages are necessary
@AKBIT Жыл бұрын
'Essential Bioinformatics' by 'Jin Xiong' book is best for beginners www.amazon.in/Essential-Bioinformatics-Jin-Xiong/dp/0521706106/ www.researchgate.net/profile/Debabrata-Samanta-5/post/Bioinformatics-Which-book-should-I-read-to-understand-bioinformatics-from-the-very-beginning/attachment/5e0ddd59cfe4a777d4002f7f/AS%3A842868579106817%401577966937429/download/Xiong+J.+-+Essential+bioinformatics-CUP+%282006%29.pdf
@akanksharout5366 Жыл бұрын
@@AKBITThank you Sir
@johannaoreilly Жыл бұрын
✋ *PromoSM*
@AKBIT Жыл бұрын
🤔
@matthewdyer7501 Жыл бұрын
You have saved my sanity. Thank you very very very much for taking the time to post this. Bless you.
@AKBIT Жыл бұрын
Thank you so much for your lovely feedback. 😊
@Estherlie1 Жыл бұрын
Thank you, the video was very helpful!
@AKBIT Жыл бұрын
Glad to hear it!
@Estherlie1 Жыл бұрын
@@AKBIT Right now I‘m trying to save the protein with the docked ligand als pdb file, but I can only save either. Could you help me out?
@AKBIT Жыл бұрын
Watch this video kzbin.info/www/bejne/mn_bkGxreL9kesk
@taimoorkhawaja4474 Жыл бұрын
plz provide link of this website in comments
@AKBIT Жыл бұрын
cactus.nci.nih.gov/cgi-bin/osra/index.cgi
@meditationrelaxingpeaceful5632 Жыл бұрын
Sir In ncbi forms to get the accession number, there is column for reference author. What to write there?
@AKBIT Жыл бұрын
Reference author means the 'name' of the data submitter.
@meditationrelaxingpeaceful5632 Жыл бұрын
@@AKBIT thanks sir! What to write in? FORWARD PRIMER NAME REVERSE PRIMER NAME Sequence Author Isolation source Isolation place
@AKBIT Жыл бұрын
Can you mention the timeline in the video where you have doubt?
@adubright6656 Жыл бұрын
Thank you Sir for the detailed explanation. Please in the WGCNA gene-coexpression network construction, which of the attributes (i.e gene name, the module colour, degree, strength, closeness, betweenness) are used in building the Cytoscape data or edge list. I have followed all the referral links you suggested but most seem to use the film -actor data. Thank you
@AKBIT Жыл бұрын
Try the data available at horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/
@user-jx7nt9bq4m Жыл бұрын
can someone help me please I can't understand clearly how to do...
@AKBIT Жыл бұрын
www.biob.in/2016/09/installing-latest-pymol-software-for.html
@sweetpie49 Жыл бұрын
Ashok sir... This was awesome
@AKBIT Жыл бұрын
Thanks for your feedback. 🙂
@haridasaravind6422 Жыл бұрын
how do we need to find out the semi global alignment that does not penalize for gaps at the beginning or the end of one of the sequences but penalizes in the middle.
@AKBIT Жыл бұрын
For finding a semi global alignment, the important distinctions are to "initialize the top row and leftmost column to zero" and terminate end at either the bottom row or rightmost column.
@nihelos931 Жыл бұрын
Do we need to minimise the energy of ligand and receptor before running the AutoDock Vina?
@AKBIT Жыл бұрын
That is your choice. If so, you have to perform prior to docking.
@W_T24 Жыл бұрын
thank you its clear 😁😁
@AKBIT Жыл бұрын
You're welcome 😊
@DiegoMariano Жыл бұрын
Hi! Nice video! Did you know some web-version of Baba-Tool? I've tried this Java version, but it's not working on my computer.
@AKBIT Жыл бұрын
You can try rna.informatik.uni-freiburg.de/Teaching/index.jsp?toolName=Smith-Waterman
@AKBIT Жыл бұрын
I have uploaded the updated JAR file. Download it from biogem.org/downloads/software/baba.jar If does not works, run through command-line as java -jar baba.jar from the location where baba.jar file is stored.
@DiegoMariano Жыл бұрын
@@AKBIT I think the problem is that some Java files are incompatible with Apple M1/M2 CPUs... I will test the first link... thank you very much ;)
@AKBIT Жыл бұрын
You're welcome 🤗