https://github.com/becksteinlab/pdb_ion_survey
A survey of ion coordination geometries in proteins.
Science Score: 13.0%
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Low similarity (4.7%) to scientific vocabulary
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Repository
A survey of ion coordination geometries in proteins.
Basic Info
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- Stars: 1
- Watchers: 2
- Forks: 1
- Open Issues: 5
- Releases: 0
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Metadata Files
README.md
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 getpdbfile 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.
Owner
- Name: Becksteinlab
- Login: Becksteinlab
- Kind: organization
- Email: obeckste@asu.edu
- Location: Tempe, AZ
- Website: https://becksteinlab.physics.asu.edu
- Repositories: 56
- Profile: https://github.com/Becksteinlab
Computational Biophysics at Arizona State University
GitHub Events
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Last Year
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Last synced: over 1 year ago
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- Total issues: 29
- Total pull requests: 2
- Average time to close issues: 3 months
- Average time to close pull requests: 2 days
- Total issue authors: 4
- Total pull request authors: 1
- Average comments per issue: 1.03
- Average comments per pull request: 0.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- orbeckst (11)
- kaceyaurum (6)
- dotsdl (1)
- nmring (1)
Pull Request Authors
- gitter-badger (1)