JeevikaSilicoBio

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@pemdorjee6727 22 күн бұрын

Plz can u tell me this chimera version cos my poc is in chinera x 1.8 version is not support these file

@robin100012001 22 күн бұрын

Great turorial

@robin100012001 22 күн бұрын

Thanks for creating this video, very informative.

@Dr.Matrujane Ай бұрын

@shahidnawaz126 Ай бұрын

good work

@deepikabv5010 Ай бұрын

For 3D confrmer which website u useing

@Chemoinformatics 2 ай бұрын

This is a useful video on how to create a structure-based pharmacophore kzbin.info/www/bejne/sH7IenWrgtt-grc

@katie9609 2 ай бұрын

When I did this with my protein, I got total 10 cavitites with MS volume of more than 100 and 11 cavities with volume less than 50. if I have to perform docking of my ligand with the cavity, how many cavitites should I choose?

@jeevikasilicobio 2 ай бұрын

You can select top 5 cavities. It would be good if you also perform blind docking to identify most probable binding site. In the case of active site/catalytic site you can easily get information from literature and sequence alignment with well characterized homologous proteins. Allosteric sites are difficult to find and characterize.

@shreem3859 3 ай бұрын

So much so so😤

@harvanshkumar9407 3 ай бұрын

FROM BBAU

@ritammondal4395 3 ай бұрын

How to save the movie

@anisaaina4067 4 ай бұрын

Thank you so much. highly recommended

@DarrellHolmes-q3u 4 ай бұрын

Moore Matthew Walker David Thompson Amy

@abelneto2980 5 ай бұрын

Hello! Thank you for you video. Do you know if chimera can generate a 2D image of the interactions?

@professorswenson3504 5 ай бұрын

Your image is so much shinier than mine and I can't figure out what I need to do. I have set the lighting and effects to full (soft is no better), and it just looks bad.

@robertcormia7970 6 ай бұрын

This webinar and narrator are understated. This is a very helpful step-by-step guided tour of ZINCPharmer. I will try to do this with some help from a student / colleague.

@pallav1995trar 6 ай бұрын

Hello sir , I have multiple chain protein . In the model loop i can only fix one chain but my protein missing residues in all chains now how to do them all togather . And when i save the modeled file . I can only see the chain which was modeled rest chain get removed in new saved file

@meenalchauhan9011 7 ай бұрын

great video, thanks! How to add scale bar for a 3D protein structure, given that I don't know the size of the protein in angstrom or nanometers?

@wasifullahdawar6962 7 ай бұрын

Command not working

@nopainnogain.sylvere416 7 ай бұрын

thank you

@abdullamamun8812 8 ай бұрын

how did you even create .xtc file which has a lot of frames? I am having issues with making multiple frames for movie making. A lot of videos show just load .xtc file but nobody even mentioned how to create .xtc file where you can have tons of frame

@jeevikasilicobio 8 ай бұрын

You will get .xtc trajectory after running MD simulation. GROMACS produces two types of trajectory files (.xtc and .trr).

@louisedwardnugroho3072 9 ай бұрын

I always get problem when showing the surface representation. It always ask me about the split command

@ES-yd1ze 10 ай бұрын

PLEASE we need that

@BALAJI-kv7xb 9 ай бұрын

Python website

@Xushdkd 10 ай бұрын

Toturial bhi dedo

@kashafrasul3952 10 ай бұрын

one click is missing when you showed the beads over 0:501 frames.. i tried in my case no such beads spread over binding pocket site?... what did i missed however i followed your steps? secondly i want to ask that how to make h.bond graph between ligand and particular residue. for example TYR81 and rename unk? can you explain in detail. and thank you this video was of great help.

@joeltorresvillena 11 ай бұрын

Hi! I love it, and I have some questions. Another video you mention that we need to create a file with all orientations that could has our ligand, so what is the next step before the virtual screening? Thanks!

@sameenagul-j2t 11 ай бұрын

Sir can you please provide me key

@Maria-yb4hx Жыл бұрын

I have one question. Will you reply?

@tehmeenanaqvi6066 Жыл бұрын

I downloaded VMD after trying for several hours and im not even able to see the main file window.... this is so sad

@c0conuts Жыл бұрын

Thank you so much

@ES-yd1ze Жыл бұрын

Hi Sir can l get covalent bond (not only reversible bonds ) interaction between the legand and protein by this software

@AmritaPBB Жыл бұрын

well explained..very useful..I have to find cavity between 3 chains of my protein, When I concatenate the chain files and give it in pdb format to castp, the job never seems to get completed..can you help me?

@AkankshaRout-h8e Жыл бұрын

As sir did download then use it

@zihaowang6505 Жыл бұрын

Why 4 anstromes? Why not 5? 3?

@suryaafrin0 Жыл бұрын

How to create npt. gro file?

@jeevikasilicobio Жыл бұрын

Using GROMACS gmx grompp command..

@DianaMValencia Жыл бұрын

Do you know a way to calculate the RMSD of the complex?

@jeevikasilicobio Жыл бұрын

Are you talking about Receptor-ligand complex? If receptor is a protein then you can calculate C-alpha or backbone RMSD. RMSD of ligand will consider all heavy atoms.

@ES-yd1ze Жыл бұрын

Can we do like Discovery studio and visualise the interaction 2D diagram ? PLEASE answer

@jeevikasilicobio Жыл бұрын

Yes, Discovery Studio Visualizer is free. You can generate a 2D interaction diagram.