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- Просмотров 1 168 186
Bioinformatics With BB
Саудовская Аравия
Добавлен 23 май 2007
This channel provides a basic to advance protocols in bioinformatics. My goal is to help you to understand highly complex biological data and improve ur computational skills in analysis Genomics, Proteomics and Transcriptomics DATA using various Bioinformatics Approaches.
Graph ggPLOT Beginner Tutorial
This video will describe you about how to create a simple graphs using ggplot2 in R program
Просмотров: 6 304
Видео
Molecular Docking VINA | Script Based Method | Multiple Ligand Docking
Просмотров 35 тыс.3 года назад
Virtual screening based on molecular docking is becoming a powerful tool in identifying lead compounds in a huge pool of small molecules.After the construction of library and preparation of receptor, each compound in the library is virtually docked into the target binding site with a docking program. The Docking aims to predict the ligand-protein complex structure by exploring the conformationa...
Protein - Protein Docking Beginner Tutorial
Просмотров 43 тыс.3 года назад
In this video, I demonstrated how to perform Protein-Protein docking using Validated docking tools such as ClusPro, PatchDock and Hex tool. ClustPro: cluspro.bu.edu/login.php PatchDock: bioinfo3d.cs.tau.ac.il/PatchDock/ Hex: hex.loria.fr/ Literature: www.nature.com/articles/nprot.2016.169 www.ncbi.nlm.nih.gov/pmc/articles/PMC2896144/ www.ncbi.nlm.nih.gov/pmc/articles/PMC1160241/
Pymol Advanced Session | Protein Ligand Interactions | Pymol Plugin Installation
Просмотров 40 тыс.3 года назад
This video session 1, will demonstrate advanced features in Pymol. Ligand and Protein Interactions Plugins Installation (Autodock, Gromacs etc.,) Protein Annotations (RMSD, Active sites, Salt Bridges etc.,) Download Pymol : pymol.org/2/ Pymol Plugins : pymolwiki.org/index.php/Category:Plugins Install Pymol Plugins: pymolwiki.org/index.php/Plugins Follow us on Instagram : bioinform...
Create Simple Graphs in R Studio | R Beginners Graphs Tutorial | Bar Plot | Scattered | Box Plot
Просмотров 69 тыс.3 года назад
In this second video of the R Beginner tutorial, I will show you how to create various plots such as bar graph, scattered plot, pie chart, box plot etc., using simple R functions. to install excel library install.packages("readxl") Facebook Group: groups/261045198486665 Instagram Page: bioinformatics.bb
Molecular Dynamics Simulation | Gromacs Installation (Win&Linux)| BeginnerTutorial | Bioinformatics
Просмотров 100 тыс.3 года назад
In this video we will learn how to install the GROMACS in windows (steps are similar in ubuntu) and I am also going to show you a beginner tutorial of MD simulation Protein in water. If your have error in installation or other troubleshoot issue join in our Facebook group : groups/261045198486665 Instagram : bioinformatics.bb Molecular dynamics is a computer simulati...
Molecular Dynamics Simulations | Gromacs Beginner Tutorial Session -2 | Bioinformatics
Просмотров 33 тыс.3 года назад
Continuation video of Gromacs tutorial Session-1, in this video we will learn about MD simulation steps and rmsd, rmsf etc., graph generation in windows. If your have error in installation or other troubleshoot issue join in our Facebook group : groups/261045198486665 Instagram : bioinformatics.bb ions.mdp : bit.ly/3k4LbtF mini.mdp: bit.ly/3bxIqxD NVT.mdp: bit.ly/3i3...
Introduction to R for Biologists | Run a Simple Program Complementary DNA
Просмотров 48 тыс.4 года назад
In this video, we will see step by step installation R and R studio in Windows, and basic introduction to RStudio. We will also learn how to write a First Program "Complementary DNA" in R RConsole: cran.r-project.org/ RStudio: rstudio.com/
PCR Primer Designing | NCBI Primer BLAST | In silico PCR primer designing and validation
Просмотров 59 тыс.4 года назад
In this video we will design a primer using NCBI Primer BLAST PCR is a commonly used method to amplify DNA of interest in many fields such as biomedical research, diagnostic testing and forensic testing. While the outcome of PCR can be influenced by many other conditions such as the template DNA preparation and reaction conditions, designing a good pair of primers is a critical factor, A genera...
Molecular Docking | Autodock VINA Virtual Screening | VINA Docking tutorial | Bioinformatics
Просмотров 83 тыс.4 года назад
Virtual screening based on molecular docking is becoming a powerful tool in identifying lead compounds in a huge pool of small molecules.After the construction of library and preparation of receptor, each compound in the library is virtually docked into the target binding site with a docking program. The Docking aims to predict the ligand-protein complex structure by exploring the conformationa...
Molecular Docking Analysis | Autodock Results Analysis | Protein Ligand Int | Pymol | LigPlot Etc.,
Просмотров 89 тыс.4 года назад
This video give you a brief on Molecular Docking (Autodock) Results Analysis, in this we showed a tutorial how to extract various scores (Binding Free Energies, RMSD, inhibition constant (Ki) ) from Docking log file of Autodock. We also, shown how to generate 2D and 3D images using various web plot form. Results Analysis Steps 1. Autodock Docking Log File Analysis 2. Save Best Docking Confirmat...
Molecular docking for Beginners | Autodock Full Tutorial | Bioinformatics
Просмотров 301 тыс.4 года назад
The molecular docking approach can be used to investigate interaction between a small molecule and a protein at the atomic level, which allow us to understand the behavior of small molecules in the binding site of target proteins, and biochemical mechanism in b’n protein and ligand molecule. This video will provide you full step by step manual on Protein-ligand docking using Autodock MGL Tools:...
Bioinformatics Methods in Identification SAS | Secondary Structure etc., (Session-2)
Просмотров 5 тыс.4 года назад
In this video we used multiple computational prediction tools to perform various protein sequence annotations such as Physio-Chemical Properties, Identification Domains, Transmemrane Regions Prediction, Secondary Structural Elements, Solvent Accessibility Surface Area etc., Input: You need provide only Single Letter Amino acid sequence in FASTA format. Sequence Retrieval Databases : www.ncbi.nl...
Bioinformatics Methods in Identification Protein Function | Domains |Trans-membrane etc.,
Просмотров 31 тыс.4 года назад
In this video we used multiple computational prediction tools to perform various protein sequence annotations such as Physio-Chemical Properties, Identification Domains, Transmemrane Regions Prediction, Secondary Structural Elements, Solvent Accessibility Surface Area etc., Input: You need provide only Single Letter Amino acid sequence in FASTA format. Sequence Retrieval Databases : www.ncbi.nl...
PIR Format File For MODELLER using HHpred (ClustalΩ)
Просмотров 2 тыс.4 года назад
This Is update/correction to my previous video on Homology modelling in generation of PIR format File. (Time: 21:40 in ruclips.net/video/k_sa9pCzstU/видео.html) One of the bioinformatics expert suggested me to do a straightforward and accurate method in creation of PIR format file, I am doing this short video on creation of PIR format file using HHpred (ClustalΩ). I will request our viewers to ...
Homology Modeling for Beginners | COVID-19 NP Protein Modeling -Session-2 | Bioinformatics
Просмотров 13 тыс.4 года назад
Homology Modeling for Beginners | COVID-19 NP Protein Modeling -Session-2 | Bioinformatics
Homology Modeling for Beginners | COVID19 NP Protein Modeling Modeller Tutorial | Bioinformatics
Просмотров 36 тыс.4 года назад
Homology Modeling for Beginners | COVID19 NP Protein Modeling Modeller Tutorial | Bioinformatics
Pymol for beginners | Basic Tutorial Molecular Visualization of Proteins | Bioinformatics
Просмотров 89 тыс.4 года назад
Pymol for beginners | Basic Tutorial Molecular Visualization of Proteins | Bioinformatics
Journal Output Style EndNote: Manual
Просмотров 3,6 тыс.4 года назад
Journal Output Style EndNote: Manual
Cytoscape PPI Network layouts | High quality network Figures for Publication | Bioinformatics
Просмотров 36 тыс.4 года назад
Cytoscape PPI Network layouts | High quality network Figures for Publication | Bioinformatics
Introduction Next Gen Sequencing - Galaxy Web
Просмотров 2,9 тыс.4 года назад
Introduction Next Gen Sequencing - Galaxy Web
Identification of nodes and edges in cluster finder
Просмотров 9585 лет назад
Identification of nodes and edges in cluster finder
Protein Protein Interactions String Cytoscape
Просмотров 32 тыс.5 лет назад
Protein Protein Interactions String Cytoscape
Sir aftr entering the ligand file name in the CMD, It is only showing the list of PDBQT files in the ligand.txt file. Vina is not running
If I may know why did you select a specific chain
sir, can you tell which scoring is used in this method, AutoDock 4 or Vian scoring function?
Hello, how does HEX do macro docking? I need your help.
Thank you Dr BB, for this video and taking time to share your expertise. You’re making a huge global impact. Best regards, Ayo (Nigeria)
Thanks for your precious information 🙏🏻♥️
finally i got my output with your tutorial, thank you sir... but i haven't get any rmd table in dlg file and i have get no more hydrogen bonds are created in analyzing conformations, may i know the reason sir and please tell me how to rectify it
beautifully done
Sir one request : plz suggest some list of good laptops for doing molecular docking project!!!🙏🏻🙏🏻🙏🏻
If you are a long time Linux/*nix user, you may backport latest gromacs from Debian Sid repository and rebuild it from the sources.
the music in the background of the video so annoying , id appracite to you is you make it without music so we can foucs on the explination well
Hi, why did you predict the transmembrane region?what is it's importance?
If you don't have coding experience or a powerful computer, you can use QuandleLabs to use all of the above tools completely online
Autogrid is not running and glg file is also not generated any solution. please help
Dear sir can you please teach me separately in Google meet for downloading the structure of protein protein interaction??
Nice
Excuse, i want to ask if i am not working on gene cloning; rather, I am conducting gene expression experiments. How can I avoid incomplete gene amplification when designing primers?
Can we run in Intel gpu
Good morning sir, I am Manohar Naik your Junior in sku from Kadiri sir , I have a doubt how can I contact you sir I have no number sir
Sir g You are the only one who not work for only to get views but to help someone
great sir thank you, the links in the description are more precious
Sir which software is used to predict the anti-cancer compound ?
3h42 and 3m0c are in complex. did you seprate them before?
why did you use hex when it was non validated
Sir , what if the ligand is not inserted to the protein
After this step, how to get 2D interactions?
I'm getting an error during running autogrid4, it's not running.
From where autogrid4 comes, I'm confused
Great video, Thanks alot and this the best lecture in docking that i have ever seen. but my question: What is the purpose of the step taken @9:10, changing the histidine hydrogens? why not +1? and why you didnt apply force field for the compounds?
Can you please tell me how to run gromacs in could Google colab platform
The best video on RUclips... thank you very much sir
Please share videos on network pharmacology, QASR and DFT for drug discovery
Fucking hindu your video and social media is a bullshit, and your teaching is boring and deficint
You just saved my undergraduate thesis research. Thank you so much!!
Im performing docking on a known active site so i limited the gridbox around the active site only. Some of the conformations i got after docking were outside the grid box. Is that normal?
Thank you so much for this helpful tutorial! I am having an issue if I can ask. When I run the command, the cmd says that access is denied.
Hi, sir , this video is very helpful to understand molecular docking with binding active site. My question is "How to know active binding site of any other protein for good result of molecular docking?????"
Thanks
Exellent ❤
Thank you professor, I want linearized vector it has 7000 basepair. I tried restrictions enzyme, but I can't find valid enzyme.so I want to make primer. Please guide me. I also tried to make primers but I can't fullfil the condition of tm, gc and no of basepair. How can I do.
sir when i want to save the GPF then i get error and shows that you must select macromolecule before writing gpf
This was SO MUCH helpful!! Thank you for the amazing explanation!
this video is a waste of time, dont even bother with it. theres thousands of better options out there
Sir Good evening sir I'm Manohar Naik from Kadiri ,your junior in SKU I have a doubt sir
When I read a paper about andrographolide as a potential inhibitor of SARS-CoV-2 main protease: an in silico approach. The andrographolide compound has a free energy of -3.09 Kcal/mol, but it shows great binding when compared to other compounds having more negative free energy values. I think about pressure, temperature, and pH in the body affecting the inhibitory process
Indeed, this variable influences the inhibitory process; it is advisable to do molecular dynamics calculations to complete the molecular docking calculations.
Make a clear cut video of cuda installation with gromacs why you skip that portion?
if its 430000 subcultures are there how to download it in sdf.
please tell me
hlo for link it showing does not exist where i get it
Why is my ligand so far away from the protein??? I know the active site of the protein
When docking, the ligand will automatically be located in the center of the box.