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?
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.
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?
Good explanation you have delivered. Thanks for that. Can you say something about pocket comparison of two different proteins
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?
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.
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
How can I find the active residues in a binding pocket?
I have one question. Will you reply?
From castp data how can i get the 3 axis x,y,z
Yes .poc file has xyz information.
confused person talking about a serious topic, shame