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 RU-vid channel focuses on computational tools and techniques which are used to understand the chemical basis of life.
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.
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
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
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!
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?
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.
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.
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...
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?
@@dianaa.valencia3910 I think if you split the frames after getting the extreme frames (eg 30 or 90) into pymol and individually show them as surface, that will work.
