This repository contains a collection of scripts and files to help in PDB retrieval for various projects. These scripts have been used to retrieve kinase-inhibitor complexes.
The PDB structures of kinases bound to FDA approved inhibitors can be found in kinase-pdbs. This folder not only contains the raw PDB structures, but also 'refined' structures that are ready for molecular simulation. The structure refinement method is detailed in kinase-refinement/README.md. The refinement procedure included, but was not limitied to protonation, missing residues modelling, and energy minimization in explicit solvent.
- The cleanest structures can be found in
kinase-pdbs/*/explicit_water_minimized/ - Automatic structure preparation is an imperfect science---use these structures with caution!
PDBfinder.py
protprep.py
kinase-refinement/minimize_explicit_solvent.py