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Shayon Bhattacharya
เข้าร่วมเมื่อ 1 ก.ย. 2008
The Channel contains LIVE sessions on theoretical and computer-assisted modelling and design of biomolecular complexes relevant for gaining mechanistic insights on biological disorders and drug development.
Vocal Cover - "Shikaayatein" from Lootera
Shikayatein is a song from the movie Lootera sung by Mohan Kanan & Amitabh Bhattacharya in the composition of Amit Trivedi.
มุมมอง: 30
วีดีโอ
"Mother" Pink Floyd Vocal cover
มุมมอง 1154 หลายเดือนก่อน
"Mother" is a song by psychedelic rock band Pink Floyd released for the album The Wall. It tells the story of Pink, an embittered and alienated rock star. As told through the song "Mother", part of Pink's sense of alienation comes from being raised by an overprotective single mother, who lost her husband, Pink's father, in World War II. The song narrates a conversation by Pink (voiced by Waters...
Prediction of chemical shift of a protein structure and dynamic ensemble by SHIFTX2 web server
มุมมอง 8724 ปีที่แล้ว
The tutorial will guide you through the step-by-step process of back-calculating chemical shift from a static structure of protein and a dynamic ensemble of protein structures by using the SHIFTX2 online web server. www.shiftx2.ca/
Predicting protein structural ensemble by fast simulation using the CABS-flex 2.0 web server
มุมมอง 3K4 ปีที่แล้ว
This tutorial will show you how to run a coarse-grained simulation of a disordered protein by using the CABS-flex 2.0 web server after obtaining a random coil structure of disordered peptide monomer as input to CABS-flex server using the NMR server pdbutil to create extended structure biocomp.chem.uw.edu.pl/CABSflex2/index spin.niddk.nih.gov/bax/nmrserver/pdbutil/ext.html
Protein structure network analysis of a peptide ensemble with Bio3D R package (Advanced)
มุมมอง 4.4K4 ปีที่แล้ว
This is a slightly advanced tutorial which will guide you to perform Dynamic Cross-Correlation Network Analysis on a predominantly disordered ensemble of the IDP amyloid-beta 42 using the R statistical computing package Bio3D. www.r-project.org thegrantlab.org/bio3d_v2/tutorials/protein-structure-networks
Sequence-based disordered domain prediction in peptides: ESpritz-DisProt and IUPRED-long web servers
มุมมอง 1.1K4 ปีที่แล้ว
The tutorial shows how to predict disordered domains from primary amino acid sequence information using two different methods: Bidirectional Recursive Neural Network (BRNN) based ESpritz-DisProt and Context Dependent prediction based IUPRED-long. The primary sequences are obtained from disordered protein database, DisProt (www.disprot.org/). old.protein.bio.unipd.it/espritz/ iupred2a.elte.hu/
Homology modelling using SWISS-MODEL web server
มุมมอง 24K4 ปีที่แล้ว
Step by step tutorial for comparative homology modelling using the SWISS-MODEL web server
Protein structure prediction by Threading: I-TASSER web server
มุมมอง 2.6K4 ปีที่แล้ว
The tutorial will guide you to predict tertiary structure of protein by threading using I-TASSER web server
Building missing residues in PDB structure as loop regions using PyMol
มุมมอง 15K4 ปีที่แล้ว
This tutorial will guide you to a step by step procedure of building or constructing annotated missing residues in a PDB structure as loop regions by using the Build Tool in PyMol, and subsequent refinement of the built loop by the ModLoop feature (loop modelling routine) in Modeller web server.
Metal ion positional optimisation
มุมมอง 4614 ปีที่แล้ว
Fun movie - a copper ion trying to fit in with a protein by optimising its position to the coordinating sites. Rendered in PyMol by using the Molecular Sculpt Tool
Viewing metal coordination states by using UCSF Chimera
มุมมอง 1.7K4 ปีที่แล้ว
The tutorial video describes how to assess the metal coordination states found in a PDB file by using the UCSF Chimera program.
How to predict protein dynamics from temperature factor using VMD?
มุมมอง 1.3K4 ปีที่แล้ว
The tutorial shows how to estimate protein dynamics from the temperature factor or B-value using the Visual Molecular Dynamics package.
How to generate a Ramachandran plot using PyMol (extension DynoPlot)
มุมมอง 8K4 ปีที่แล้ว
This tutorial will guide you step by step to generate a Ramachandran plot of protein residues by using the DynoPlot extension in PyMol.
Protein-ligand docking with AutoDock Vina and UCSF Chimera
มุมมอง 27K4 ปีที่แล้ว
The tutorial will guide you through the step-by-step procedure to dock a small molecule ligand amino acid (L-Asp) to a protein receptor (AspRS) by using AutoDock Vina integrated with Chimera. Model system: Aspartyl-tRNA-synthetase.
How to rename chain ID and residue name using PyMol?
มุมมอง 7K4 ปีที่แล้ว
The video tutorial will guide you to rename chain ID 'A' to 'B' and residue name of the ligand 'AMO' to 'ASP' using PyMol package. Model system: aspartyl-tRNA-synthetase. Alter selection or object in PyMol: pymolwiki.org/index.php?title=Alter&redirect=no Selection keywords: pymolwiki.org/index.php/Selection_Algebra
How to edit molecular fragments and *invert* the stereochemistry with UCSF Chimera?
มุมมอง 2.3K4 ปีที่แล้ว
How to edit molecular fragments and *invert* the stereochemistry with UCSF Chimera?
How to obtain a PDB structure file from the Protein Data Bank?
มุมมอง 2.9K4 ปีที่แล้ว
How to obtain a PDB structure file from the Protein Data Bank?
How to perform basic operations on a molecular structure using VMD?
มุมมอง 9K4 ปีที่แล้ว
How to perform basic operations on a molecular structure using VMD?
VERY GOOD
We can clear the work by clicking on file then close session instead of closing the software.
very informative, very demure. thank you so muchh
I need help in docking
in my case command line residues are not showing and also binding pockets are not showing the residues.. what should I do?
Even after filling the gap in between the protein sequence, I am getting broken lines in my structure. How to fix it?
how can i get the link to download dynoplot
How do I recognize amino acids in the residues of binding site for a different proteins?
Great singing my friend!! Like 2
Thanks for listening 🎧
How do you know what net charge to add to the ligand during preparation? Should it always be 0? For example, I have downloaded ATP from PubChem. It has several deprotonated phosphate groups, do I need to specify in Chimera the negative3 charge? Thank you!
Sir why I can't paste the smiles from pubchem to ucsf chimera
I have a.a residues more than 5000, what to do in this case?
I have a.a residues more than 5000, what to do in this case?
@shayonbh_molmod hi can you please let me know how can i perform cross-correlation for a complex a receptor with small molecule ligand. as ligand has only one residue and donot contain CA . thank you.
I love you
For IUpred which score should I really look into the Iupred score or the ANCHOR score for predicting the IDR
I am new to bioinformatics, my question is what if % identity and Query coverage is less but the GMQE and Qmean score is good?, which factors are more important than the other when deciding on a good model? Again what does it mean when your swiss model has no QSQE score?
Can you explain the spaghetti model more? What do the different colors show ?
Hi sir,what should i do if swissmodel cannot find any matching template,because i am trying to predict a heteropentamer
Very best…! Amazing
During registration process.... We have to submit a academic e mail id.. But i don't have.... What should i do
Hello sir. what should be the selection parameter to be taken in to consideration for selecting template and what should be the percent identity for the template?
Having laboured through 3 other YT tutorials on this exact same topic, I can say this is far and away the best tutorial. I am left wondering if the other presenters actually knew what they were talking about. This tutorial is authoritative, straightforward and well presented - excellent stuff. Thank you.
Congratulations on the tutorial: I have a question How do I search for homology of a ligand that has no Fasta sequence?
so good sir
Great tutorial video. Thank you for creating this content.
I have dipole.xvg file for a protein , generated using gromacs. I will be a grt help if u tell me how to visualize THAT dipole moment along with protein in vmd!!!
There is an error shown - [Error 13] permission denied: complex.pdbqt. How to rectify???
Sir, is it necessary to validate proteins secondary structure using Prochek after loop refinement?
Plz make a video on how to do metal complexes docking
How to add atoms on missing residues?
i hope that you kindly share the R code sir, or your gituhub which posted about this code
It was very useful, thanks so much :")
Thank you. Please how can I get my binding site for command prompt
Thank you sir for the amazing video.
Good afternoon, could you send me the link you put in the url, please.
If I pass it’s coz of you thanks
Can we change Residue 1 to Residue number 96 but amino acid residue of whole chain is remain same as previous
Very informative lecture.
actual docking: 10:37
Thanks very much for this tutorial professor. Please Sir after doing redocking, if your ligand aligns with the cocrystallised ligand but doesn't have a good RMSd value which parameters can you modify to have a perfect alignment which will lead to a good RMSd value? Thanks
Can we change or alter the residues numbering in pymol?
Thank you very much. Could you let me know, how I can do this when missing resides are in the middle of protein?
Please Make a tutorial on complete MD Simulation..
There are few great tutorial links on complete MD simulations already. Please have a look at this one with Gromacs: th-cam.com/video/rYZ1p5lXNyc/w-d-xo.html
Great job sir
How download auto dock vina.last step auto dock does no work.for window 10
Hi. How can I replace one metal with another on chimera?
Thank you Shayon
THANK YOUUUUUUUUUUU :')))))))))))))))))))))))
Thank you so much. Helped me a lot