Hi. I am a doctoral student.
The binding structure is predicted using specific protein and peptide sequences. By the way, each time I do, I have to worry about how to interpret it because the result is different.
The program used is the web-application CABS-dock. Put the PDB number (only the protein receptor part) in it, put in the specific peptide and wait for 4 ~ 5 hours.
I want to get data from 10 predicted values attached to the desired spot (the middle part of the receptor) and sort out the result when it comes out.
I do not know which value is correct because the result is different every time. I am studying the structural protein field because it is not a specialized field.
I do not understand the meaning of the terminology of CABS-dock. For example, "cluster-density", "RMSD(root-mean-square deviation), average RMSD, max RMSD"
Currently, the structure of the peptide is not known, so I use a prediction program to identify the binding site.
If you have a program that is more accurate and reproducible than the CABS-dock, please let me know.