https://github.com/becksteinlab/pdb_ion_survey

A survey of ion coordination geometries in proteins.
https://github.com/becksteinlab/pdb_ion_survey

protein-structure proteins science

Last synced: 3 months ago
JSON representation

A survey of ion coordination geometries in proteins.

• Host: GitHub
• URL: https://github.com/becksteinlab/pdb_ion_survey
• Owner: Becksteinlab
• License: gpl-3.0
• Created: 2015-11-24T00:14:50.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2022-06-17T22:09:42.000Z (almost 3 years ago)
• Last Synced: 2025-01-06T10:48:27.444Z (5 months ago)
• Topics: protein-structure, proteins, science
• Language: Python
• Homepage:
• Size: 2.74 MB
• Stars: 1
• Watchers: 3
• Forks: 1
• Open Issues: 5
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        
# Protein Ion Coordination Survey

[![Join the chat at https://gitter.im/Becksteinlab/PDB_Ion_Survey](https://badges.gitter.im/Becksteinlab/PDB_Ion_Survey.svg)](https://gitter.im/Becksteinlab/PDB_Ion_Survey?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)

As part of the [BioXFEL Ed Scientific Villages at ASU](https://www.bioxfel.org/education/high-school-learning-communities) program, [@kaceyreidy](https://github.com/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](http://www.pdb.org). [MDAnalysis](http://www.mdanalysis.org) 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.