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Primal Bioinformatics
India
Приєднався 18 жов 2011
Amplify your bioinformatics knowledge with simple videos!
We release weekly videos to help you create better learning and understanding to maximize your knowledge in various topics so that you can harness the power of Bioinformatics to GROW your career on autopilot.
We release weekly videos to help you create better learning and understanding to maximize your knowledge in various topics so that you can harness the power of Bioinformatics to GROW your career on autopilot.
Drawing and Optimizing Drug Structures with Avogadro - Complete Tutorial
Welcome to Primal Bioinformatics! In this tutorial, we explore Avogadro, a powerful tool for drawing and optimizing drug structures. This step-by-step guide will cover:
Introduction to the Avogadro interface
Drawing simple molecules like methane
Importing and optimizing complex molecules
If you found this tutorial helpful, please like and subscribe to Primal Bioinformatics for more tutorials on bioinformatics tools and techniques. Thanks for watching!
Timestamps:
Introduction
Avogadro Interface Overview
Drawing Simple Molecules
Importing Complex Molecules
Optimizing Molecular Structures
Conclusion
Introduction to the Avogadro interface
Drawing simple molecules like methane
Importing and optimizing complex molecules
If you found this tutorial helpful, please like and subscribe to Primal Bioinformatics for more tutorials on bioinformatics tools and techniques. Thanks for watching!
Timestamps:
Introduction
Avogadro Interface Overview
Drawing Simple Molecules
Importing Complex Molecules
Optimizing Molecular Structures
Conclusion
Переглядів: 115
Відео
Drawing Drug Molecules with MarvinSketch: Aspirin, Paracetamol, Ibuprofen, Caffine, Atorvastatin...
Переглядів 1063 місяці тому
Welcome back to my channel! In this tutorial, I'll show you how to draw some common drug molecules using MarvinSketch. We'll cover Aspirin, Paracetamol, Ibuprofen, Caffeine, Atorvastatin, and Amoxicillin. If you're new to MarvinSketch, be sure to watch my previous video where I cover the basics of the MarvinSketch interface [link in the description]. Timeline Introduction Aspirin (Acetylsalicyl...
Exploring the MarvinSketch Interface: A Comprehensive Guide
Переглядів 563 місяці тому
Welcome to Primal Bioinformatics! In this detailed tutorial, we’ll take you on a tour of the MarvinSketch interface, a powerful tool for drawing and editing chemical structures. Whether you’re new to MarvinSketch or looking to refresh your skills, this video covers everything you need to know about its interface. Don't forget to like, share, and subscribe for more informative videos! Timeline: ...
Drawing Drug Molecules with ChemSketch: Aspirin, Paracetamol, Ibuprofen, Caffeine, Atorvastatin..
Переглядів 1273 місяці тому
Welcome back to my channel! In this tutorial, I'll show you how to draw some common drug molecules using ChemSketch. We'll cover Aspirin, Paracetamol, Ibuprofen, Caffeine, Atorvastatin, and Amoxicillin. If you're new to ChemSketch, be sure to watch my previous video on the basics of the Throughout this video, I'll also share interesting facts and highlight the key functional groups for each dru...
Mastering Homology Modeling with Swiss-Model: A Complete Guide Including Validation
Переглядів 2483 місяці тому
Explore the intricacies of protein structure prediction in our comprehensive tutorial on homology modeling using Swiss-Model. This video provides a step-by-step guide on predicting the 3D structure of Aflatoxin B1 aldehyde reductase member 4 (Q8NHP1) from Homo sapiens. Learn to retrieve protein sequences, submit them to Swiss-Model, interpret essential metrics like GMQE and QMEAN scores, and va...
Mastering Multiple Sequence Alignment with Clustal Omega & MUSCLE | Bioinformatics Tutorial
Переглядів 1613 місяці тому
Unlock the power of bioinformatics with our step-by-step tutorial on multiple sequence alignment using Clustal Omega and MUSCLE! In this video, we'll guide you through: Introduction to Multiple Sequence Alignment (MSA) Understanding Insulin: Sequence Information and Structural Features Downloading Insulin Sequences from UniProt Performing MSA with Clustal Omega Interpreting Clustal Omega Result...
Sequence Similarity Search Using BLAST: Step-by-Step Guide
Переглядів 1233 місяці тому
In this tutorial, we dive deep into the world of sequence similarity search using the BLAST tool. Join us as we explore how to use BLAST to find similar protein sequences, understand sequence alignments, and interpret BLAST results effectively. We’ll also look at how changing the database and scoring matrices can impact your results, and analyze homologous, orthologous, and paralogous relations...
Exploring Biological Sequence Data and File Formats | UniProt & NCBI Tutorial
Переглядів 863 місяці тому
Welcome to our Bioinformatics Tutorial Series! In this video, we'll explore the essential aspects of bioinformatics resources, focusing on UniProt and NCBI. This exercise aims to familiarize you with key bioinformatics tools and develop your skills in retrieving and analyzing biological sequence data, interpreting protein functions, and understanding the significance of various protein modifica...
Exploring the ChemSketch Interface for Drawing Drug Molecules
Переглядів 1033 місяці тому
Welcome to the second video in our series on using ChemSketch for drawing 2D and 3D small molecular drug candidates. In this tutorial, we'll dive into the ChemSketch interface and focus on the essential tools and options that are crucial for drawing drug molecules. Whether you're a student, researcher, or professional, this video will help you create accurate molecular structures with ease. In ...
How to Download and Install ChemSketch, MarvinSketch, and Avogadro for Molecular Drawing
Переглядів 9003 місяці тому
Welcome to my channel! In this video, I will guide you step-by-step through the process of downloading and installing three essential tools for molecular drawing and 3D modelling: ChemSketch, MarvinSketch, and Avogadro. These tools are invaluable for students and professionals in chemistry and drug design. Follow along to get all three software up and running on your computer in no time!
Drawing 2D and 3D chemical structures
Переглядів 643 місяці тому
Drawing 2D and 3D chemical structures
de novo ligand deisgn using LigBuilder
Переглядів 1923 місяці тому
de novo ligand deisgn using LigBuilder
advanced homology modelling using modeller - protein with ligand
Переглядів 1893 місяці тому
advanced homology modelling using modeller - protein with ligand
Protein-protein docking demonstration by Dr. Saraboji
Переглядів 2,9 тис.Рік тому
Protein-protein docking demonstration by Dr. Saraboji
Flexible Protein Ligand Docking using AutoDock
Переглядів 4,3 тис.Рік тому
Flexible Protein Ligand Docking using AutoDock
Rigid Protein Ligand Docking using AutoDock
Переглядів 1,3 тис.Рік тому
Rigid Protein Ligand Docking using AutoDock
Advanced Homology Modelling using Modeller
Переглядів 851Рік тому
Advanced Homology Modelling using Modeller
Intermediated Homology Modelling using Modeller
Переглядів 687Рік тому
Intermediated Homology Modelling using Modeller
Drug - biotransformation and CYP450 cycle
Переглядів 48Рік тому
Drug - biotransformation and CYP450 cycle
Drug - volume of distribution and introduction to metabolism
Переглядів 30Рік тому
Drug - volume of distribution and introduction to metabolism
Computer Aided Drug Design and Role of X-ray crystallography in SBDD
Переглядів 84Рік тому
Computer Aided Drug Design and Role of X-ray crystallography in SBDD
Very very very good tutorial but resolution is very low Maybe I need to contact with you on WhatsApp 🎉🎉
Thanks and very well you can WhatsApp me @ 9600420006
you forgot to give htvs files ?
I will share it. Send me your email address.
thank you
Why in my results, local quality estimation plot and other plots are not showing?
You are using the online server right?
Dear Sir ...the whole system is shutting down after select from the string
Try to install lower version of ADT
nice lecture sir, may i know your specialization
Computational chemistry and drug design
From where did you get box parameters loke x center y center z center values?
We have to cover the entire binding pocket. No default value. The grid box value will change from protein to protein.
Very good tutoial PLEASE How to use modeller with chimera need simple tutorial For that
I will make one.
what is pylab? i tried to modify the plot_profiles.py like you did and use IDLE but it is not running? i have a mac os and have anaconda/pycharm installed? or how to use the command prompt for it? or how should i edit the plot_profiles.py file? Please help me
Do you still need help?
can u share the commands that are shown on right side
DO you still need it?
@@primalbioinformatics yes
I am making another flexible docking video. I will upload it in a day or two. In which i will give those commands in the description.
how about adding ordered water from the template to the query sequence model?
You can follow the same procedure used for modelling along with ligands. The water molecules of your interest should be included in the template PDB file.
Sir, from where I can get the python script used to model protein with ligand. Thanks
Mention your email and i will send you
thanks for the ssuch an informative video , but i have one query that is how did you get pbd_95.pir file . please explain here
salilab.org/modeller/supplemental.html
How to identify active site for any protein or DNA.
There are many online servers to predict the protein binding pockets. You may try with sts.bioe.uic.edu/castp/index.html?3trg
@@primalbioinformatics is the things same for DNA? My compounds are rigid I have done blind docking with DNA. One question main what changes one may observe if with same compound and protein both flexible and rigid docking is tried?
@@SimranSharma-i8iRegarding your second question, proteins are basically flexible in the biological environment, but in order to reduce the computational intensity required for the docking simulations, we keep the protein rigid. Flexible docking mimics the real nature of the protein to some extent but not completely (flexibility is given only for a few amino acids). You can provide complete flexibility for the protein and study the protein-ligand complex interactions through a Molecular Dynamic Simulations study. The binding affinity obtained through the rigid and flexible docking may change sometimes but not always.
@@primalbioinformatics Hi, thanks for replying I am facing one problem how things will change If I am docking with A-DNA. Actually, I randomly chose one DNA 3Qk4 and with that, my compounds were showing docking but now after finalizing all the data I am not finding any report with that DNA and that is A-DNA. But with that it is showing interaction. Can I submit my paper with that .
@@SimranSharma-i8i I need more details to answer you. Can you let me know what is the rationale for choosing this DNA and performing docking? Can you Whatsapp me @ 9600420006? I don't check youtube comments frequently.
thank you for making this video sir
Dear sir,during the step select from string, I choose 'ARG24,ARG47',and click add,but when I click choose torsion and currently selected, the whole programme is shutdown.what can I do to solve this problem?
Do you still have this problem?
@@primalbioinformatics I have this problem know What should I do??
@@ES-yd1zeWhich version of AutoDock Tools do you use?
@@primalbioinformatics yes!The Autodocktools version I used is 1.5.7,Dec_19_18
I have the same problem. As soon as I choose "residue," the whole programme is shutdown
thanks 👍🏻
Sir @primalbioinformatics can you please upload covalent docking tutorial
One of the best teacher
Perfect lecture for the subject
Respected sir, plz upload the next video of the docking series, and also tell us about the picture quality in the docking for publication purposes. Thank you
Sir in my . Ali file i have 446+... Hetero atoms are present in 511... What shall I put while editing the Ali file?
Kindly share your .ali file to karthi.bioinfo@gmail.com
@@primalbioinformatics sir i have sent you mail. Could you please have a look.
@@Deevena970 Hi. I have emailed you the model. Kindly check and let me know if any queries.
@@primalbioinformatics Thank you so much sir.
Sir please upload qsar analysis 🙏
You need 2D or 3D QSAR analysis?
@@primalbioinformatics Everything Sir, really it will be helpful for many people there is no proper practical video in entire youtube. Thanks for your reply
@@sanjaisrao484 Ok. I will upload it next week.
@@primalbioinformatics Thanks sir🥺
Respected sir, make a video on docking result visualization like 3D image and 2 D image
I am uploading next week.
nice explation sir
Thanks and welcome
Came out well!
Not newly recorded. Previous year course lecture.