Active site using castpfold

Question

[Ria]

How to find grid coordinates for docking using castpfold? As castp was not working I used castpfold website which is an advanced version of castp. In results there was a file called poc file which contained all residues and their residue number, pocket etc. How to select which pocket i need? And then how to get grid coordinates of that pocket needed for docking.? My protein structure don't have ligand with it. Only the cleaned protein structure.

[Mensur Dlakic]

Please don't take my comment the wrong way.

Docking ligands is a serious endeavor that includes many preparatory steps, a use of highly sophisticated software, and a good deal of expertise to interpret the results. If you don't know how to get residue coordinates, or pocket coordinates, this procedure may be beyond your abilities. It is impossible for anyone to guide you through the whole process via this site or any other. I suggest you find someone locally who can teach you these things, or search through the internet for a step-by-step tutorial. For example, I know that AutoDock and Vina have very clear tutorials that explain all the steps.

Answer 1

[dthorbur]

This is very similar to your recent post - if you aren't going to provide the protein example for a reproducible example we cannot help very much. You don't even need to use the protein of interest, another similar protein could be used if you are that worried about secrecy.

There is also information about how to identify the pocket, and how they're annotated in the tutorial for castpfold. Have you looked at that? The output identifies which residues are in the predicted pockets. You can then find the X,Y, and Z coordinates in a given PDB/mmCIF file for each atom in those residues.