How to select the right protein structural data from PDBbind database as there are multiple options?

Question

[entropy]

I am planning to virtually screen and get binding scores of my protein of interest and all the compounds in the REAL database.

As an input to the structural based virtual screening (SBVS) pipeline (for example using AutoDock as the scoring funciton in it), I need to input structural data of my protein of interest. However, in PDBbind database, there are multiple options to select and get the structural data for my protein.

Then the question is, which specific one I need to select and download for such a usage? I cannot run all of them as it is very expensive for even one run.

For example, when you input EGFR into the search box of https://www.rcsb.org/ it results 409 Structures Link to access this search.

I have expertize only in computational part and not know much about the biology for this specific problem. Therefore, I am not sure which structure to select.

Thank you for yor helps.

Answer 1

[jgreener]

You will have to work out the biological question you want to answer with such a screen. That might make it clearer which structure to choose.

Look for one in the right oligomeric state you want to study, and consider which ligands/co-factors you are okay with being bound. Then choose a structure with no missing residues near the binding site and the highest possible resolution.