Becksteinlab / PDB_Ion_Survey

A survey of ion coordination geometries in proteins.

Protein Ion Coordination Survey

As part of the BioXFEL Ed Scientific Villages at ASU program, @kaceyreidy is building a reusable data acquisition and analysis pipeline to characterize the interactions between ions and proteins.

The input data are crystal structures from the Protein Databank. MDAnalysis is used to analyze the data. The initial focus is on a statistical analysis of the coordination numbers of ions, in particular oxygen-cation interactions.

How to Use

• Use get_proteins to search the PDB for molecules of a certain type with a specified ion.
• Use get_pdb_file to download pdb files from the PDB.
• Use en to create radial distributions for oxygen atoms around an ion.
• Use cume to create a cumulative radial distribution function for oxygen atoms around an ion.
• Use gee to create a density radial distribution function for oxygen atoms around an ion.
• Talk to Martin Blech to use unparse or _emit.