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JeevikaSilicoBio
India
เข้าร่วมเมื่อ 27 ส.ค. 2016
During the last three decades, the fields of biology and chemistry have undergone a massive transformation due to involvement of computers and information technology. This TH-cam channel focuses on computational tools and techniques which are used to understand the chemical basis of life.
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มุมมอง: 85
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FROM BBAU
How to save the movie
Thank you so much. highly recommended
Moore Matthew Walker David Thompson Amy
Hello! Thank you for you video. Do you know if chimera can generate a 2D image of the interactions?
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.
Good explanation you have delivered. Thanks for that. Can you say something about pocket comparison of two different proteins
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.
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
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?
Command not working
thank you
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
You will get .xtc trajectory after running MD simulation. GROMACS produces two types of trajectory files (.xtc and .trr).
I always get problem when showing the surface representation. It always ask me about the split command
PLEASE we need that
Python website
Toturial bhi dedo
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.
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!
Sir can you please provide me key
I have one question. Will you reply?
I downloaded VMD after trying for several hours and im not even able to see the main file window.... this is so sad
Thank you so much
Hi Sir can l get covalent bond (not only reversible bonds ) interaction between the legand and protein by this software
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?
As sir did download then use it
Why 4 anstromes? Why not 5? 3?
How to create npt. gro file?
Using GROMACS gmx grompp command..
Do you know a way to calculate the RMSD of the complex?
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.
Can we do like Discovery studio and visualise the interaction 2D diagram ? PLEASE answer
Yes, Discovery Studio Visualizer is free. You can generate a 2D interaction diagram.
how you have created npt.gro file?
How can I find the active residues in a binding pocket?
Hello sir can u please tell me it is necessary to save all models in a file or is it ok if we save only single model
Very useful information for beginners. Thank you!
Nice one! Thank you
Hello sir Small molecules drawn using pubchem sketcher can be used for docking ?
Yes...
Thank you. Can you please write once again how to save the overlap file
How did the ligand get there
Can you please tell me if there are any free softwares for receptor based pharmacophore modelling and virtual screening??
Simulation time?
100 ns...
Good
if there is no pdb structure of our wild and mutant protein, then what we will do ?
You can build models by homology modeling. AlphaFold is also an option.
nice explanation sir
Sir is there any scope for training under Jeevika Bio ?
Yes
Sir I want to enrol. Please let me know the procedure
Hello Sir, how to enrol for training under jeevika silico bio? Kindly guide. Thank you and regards
I find your tutorials very helpful. Thank you so much.
Thank you Diana..
Hello Sir, How to get in touch with your institute?
You can contact me: kumarviks1984@gmail.com
I have a quick question. Does model/refine loop option in Chimera do any optimization or refinement?
Yes, Chimera uses either locally installed Modeller software or web service ( Modeller) for the modeling and refinement of loop region(s). Script first generate an initial model and then several loop conformations are generated based on initial loop conformation. So optimization algorithm is active in this case. You can click on the given link for more details.. salilab.org/modeller/manual/node499.html
@@jeevikasilicobio Does it apply optimization to only modeled part? I want to keep the rest of the protein as it is. So in such a case, can I use Modeller in Chimera or should I write a script for it?
@@ecemgungor6208 You can keep rest of the protein as it is. Just select 1 residue adjacent to the missing regions to move.... You can use the web service, no need to write a script.
@@jeevikasilicobio Thank you so much! Please keep recording videos on MD and analysis/modeling! It is very useful for beginners! Thanks!
Which inhibitor was it?
Sir, Can you please suggest how can we calculate binding energy or stability of this mutated complex ? I will be very thankful if you can make a video on further analysis of this mutated complex regarding their stability, change in activity after mutation of protein. I am very eager to know how the mutation in one protein affect its interaction to other protein. Thank you
Hii Vijay, Thank you for your comment. Mutations within or near active site of protein may affect their activities and stabilities. If mutation is located at protein-protein interaction(PPI) interface then it can stabilize or destabilize the PPI. SARS-CoV2 RBD-human ACE2 complex is a good example... I will upload a video on it...
How could I merge non polar hydrogen
Dear sir when your protein has both missing residues in loop region and in intermediate regions which option do you choose for modelling, All missing residues?
Yes, in that case, you can use all missing residues options
Great tutorial thanks à lot.
Glad you enjoyed it!