How can I place a molecule structure in the program when I already have my protein and get a binding site prediction? What file format should the molecule have and where could I find it or who can I make such a file myself? Thank you for the video
i want to visualize a protein protein complex docked pdb file by zooming the specific binding sites for publication.I already did the binding in pymol.But when i try to zoom the binding sites into word the figure is not very clear to see.So kindly help me on this.Thanks
excellent video. I tried to install the LISICA plugin for pymol and I was not able to load it because I got the following error: Unable to initialize plugin 'lisica' (pmg_tk.startup.lisica). I appreciate that you can help me solve the problem.
when i try to visualize the hydrogen bond between to interected protein,and wanted to show the residues,there i get a problem and the problem is-sometimes for the sticks the residues name cannot show properly.Is there any way to move or edit the interected residue name by my suitability
@@jaannawaz2007 Hi sir, I checked, but there is no way of finding the "undo" plugin right now, not sure why but the link was blocked. Also, the Autodock plugin lost its downloadable link. If you don't mind, could you please share both of these? Many thanks!
@@jaannawaz2007 i want to know something about haddock. In hadock how the best binding was calculated? Is it seeing by hadock score or PRODEGY(based on delta G) score??
Nice presentation sir
could you please do protein -protein interaction
Hello, I want to check the interaction between 2 protein sequences ( one from virus and one from vaccine). How can I do so?
How can I place a molecule structure in the program when I already have my protein and get a binding site prediction? What file format should the molecule have and where could I find it or who can I make such a file myself? Thank you for the video
Thanks sir
Welcome
How to find and install external plugins
How can I get the pdf files for the tutorials. Would be better if we can do the tutorials parallelly with the same pdbs.
i want to visualize a protein protein complex docked pdb file by zooming the specific binding sites for publication.I already did the binding in pymol.But when i try to zoom the binding sites into word the figure is not very clear to see.So kindly help me on this.Thanks
this need to be paid version or can be done on the education version only
can you comlete this hrase" please show sticks , by ...... protein within ......" i can t find it in this video
excellent video. I tried to install the LISICA plugin for pymol and I was not able to load it because I got the following error:
Unable to initialize plugin 'lisica' (pmg_tk.startup.lisica). I appreciate that you can help me solve the problem.
contact admin of plugin ... www.cmm.ki.si/konc/
@@jaannawaz2007
I think the website has been improved and moved to insilab.org/
Hi sir, can you please tell me about the long chain at 26.13
What is the pdb id for the molecule used for protein-ligand interaction?
Hello, would you please send a link for the pdbs you used in this tutorial
How to prepare protein ligand docking complex?
See professor BB's other videos on how to use autodock software.
How did you determine where in space to precisely place the ligand relative to protein?
use the autodock software to screen for the active site of the protein. Professor BB has another video on this topic.
when i try to visualize the hydrogen bond between to interected protein,and wanted to show the residues,there i get a problem and the problem is-sometimes for the sticks the residues name cannot show properly.Is there any way to move or edit the interected residue name by my suitability
may be the font size is too small... type this command on shell --- set label_size, 16
would you please make a link to commands used in this tutorial
Hi
I have trouble installing autodock plugin on pymol.
I think the plugin code is in python2 but pymol is using python3.
Anyone can please help me?
Agree.. we dont have updated version of plugin, write an email to developer www3.mpibpc.mpg.de/groups/de_groot/dseelig/index.html
sir can we have video tutorial for circos, maybe for next videos
soon
Hello. Are you available for hire to work on a short but advanced pymol project?
Sorry, no... i am just sharing my knowledge, i am not free lancer .. any way thanks for ur offer
Please, How can we build up 3D protein structure from amino acid sequence?
you can use modeller 10.1 using homology protein as a template
With alphaFold
Where do we get the various plugins, like the one you have in your folder?
check links that i provided in the in the description box
@@jaannawaz2007 Hi sir, I checked, but there is no way of finding the "undo" plugin right now, not sure why but the link was blocked. Also, the Autodock plugin lost its downloadable link. If you don't mind, could you please share both of these? Many thanks!
How can i see salt bridges in pymol?
Pymol rightside pannel >show>disulfides>spear
@@jaannawaz2007 thanks but i am asking about salt bridegs ??
@@johirislam8174 check this link www.researchgate.net/post/How_to_see_Salt_Bridges_in_Pymol
@@jaannawaz2007 i want to know something about haddock. In hadock how the best binding was calculated? Is it seeing by hadock score or PRODEGY(based on delta G) score??
Hmm so 2.5 and 5 angstrom interactions hmm
..._hbonds ... is what I cannot see
Sir, can I get your email id I want to ask one question