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.
Thank you.
I think that RMSD needs some clarification to in the context of docking. To calculate it, two atom structures are needed that are somehow supposed to be aligned or similar. It is not clear to me what is actually compared in the docking context, maybe it refers to re-docking and then the software calculates the distance between the experimental docking pose and the predicted docking pose. I'd suggest OP to have a look at the documentation of the software and check which structures are actually are compared.
Yeah that's probably a good point. I assume it would calculate ligand-pocket binding distances (if not all-vs-all), but I'm no expert. a-Carbon to a-Carbon is the default method for protein superimposition studies which I'm much more familiar with.