deerpredict
Software for the prediction of DEER and PRE data from conformational ensembles.
Science Score: 57.0%
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○CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
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✓DOI references
Found 4 DOI reference(s) in README -
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Links to: zenodo.org -
○Committers with academic emails
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Organization kull-centre has institutional domain (www1.bio.ku.dk) -
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○Scientific vocabulary similarity
Low similarity (13.1%) to scientific vocabulary
Keywords
Repository
Software for the prediction of DEER and PRE data from conformational ensembles.
Basic Info
Statistics
- Stars: 12
- Watchers: 4
- Forks: 3
- Open Issues: 0
- Releases: 5
Topics
Metadata Files
README.md
DEER-PREdict
Overview
A package for double electron-electron resonance (DEER) and paramagnetic relaxation enhancement (PRE) predictions from molecular dynamics ensembles.
Installation
To install DEER-PREdict, use the PyPI package:
bash
pip install DEERPREdict
or clone the repo:
```bash git clone https://github.com/KULL-Centre/DEERpredict.git cd DEERpredict
pip install -e . ```
The software requires Python 3.6-3.9.
In case of dependency issues, consider installing FRETpredict in a new environment
bash
conda create -n myenv python=3.9 pip
conda activate myenv
pip install -e .
Documentation
Testing
Run all the tests in one go
```bash cd DEERpredict
python -m pytest ``` or run single tests, e.g.
```bash cd DEERpredict
python -m pytest tests/testPRE.py::testACBP python -m pytest tests/testDEER.py::testT4L ```
Example
Example of how to run PREpredict to calculate the intensity ratios and PRE rates for PDB code 1NTI (20 conformations) using the BASL MMMx rotamer library (see notebook). Available libraries for MTSSL, BASL, and MA-proxyl probes are listed in DEERPREdict/lib/libraries.yml.
python
PRE = PREpredict(MDAnalysis.Universe('1nti.pdb'), residue=36, libname='BASL MMMx',
tau_t=.5*1e-9, log_file='calcPREs/log', temperature=298, z_cutoff=0.05,
atom_selection='H', Cbeta=False)
PRE.run(output_prefix='calcPREs/BASL', tau_t=.5e-9, delay=10e-3,
tau_c=2e-09, r_2=10, wh=750)
Example of how to run PREpredict to calculate the intensity ratios and PRE rates for PDB code 1NTI (20 conformations) using the MA-proxyl MMMx rotamer library.
python
PRE = PREpredict(MDAnalysis.Universe('1nti.pdb'), residue=36, libname='MA-proxyl MMMx',
tau_t=.5*1e-9, log_file='calcPREs/log', temperature=298, z_cutoff=0.05,
attract_scaling=2, atom_selection='H', Cbeta=False)
PRE.run(output_prefix='calcPREs/MAP', tau_t=.5e-9, delay=10e-3,
tau_c=2e-09, r_2=10, wh=750)
License
This project is licensed under the GNU General Public License version 3.0 (GPL-3.0). However, the rotamer libraries in DEERPREdict/lib are modified versions of those from the MMMx program, and these modified libraries are licensed under the MIT License, as detailed in the LICENSE file. The rest of the project is licensed under the GPL-3.0, and any combination of GPL-3.0 licensed files with those under the MIT License will be subject to the terms of the GPL-3.0.
Authors
Kresten Lindorff-Larsen (@lindorff-larsen)
Article
Tesei G, Martins JM, Kunze MBA, Wang Y, Crehuet R, and Lindorff-Larsen K (2021) DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles. PLOS Computational Biology 17(1): e1008551. https://doi.org/10.1371/journal.pcbi.1008551
Owner
- Name: Linderstrøm-Lang Centre for Protein Science, University of Copenhagen
- Login: KULL-Centre
- Kind: organization
- Location: Copenhagen, Denmark
- Website: https://www1.bio.ku.dk/english/research/bms/research/llc/
- Repositories: 8
- Profile: https://github.com/KULL-Centre
GitHub Events
Total
- Watch event: 1
- Push event: 5
Last Year
- Watch event: 1
- Push event: 5
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| gitesei | g****i@g****m | 67 |
| Ramon Crehuet | r****t@i****s | 9 |
| João M. Martins | m****l@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: over 1 year ago
All Time
- Total issues: 3
- Total pull requests: 2
- Average time to close issues: 2 days
- Average time to close pull requests: about 1 hour
- Total issue authors: 3
- Total pull request authors: 2
- Average comments per issue: 2.33
- 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
- ParkerPBD (1)
- AlexanderJussupow (1)
- samlobe (1)
Pull Request Authors
- joaommartins (1)
- gitesei (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 99 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 13
- Total maintainers: 1
pypi.org: deerpredict
A package for DEER and PRE predictions based on molecular dynamics ensembles. Can be installed with pip.
- Homepage: https://github.com/KULL-Centre/DEERpredict
- Documentation: https://deerpredict.readthedocs.io/
- License: GPLv3
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Latest release: 0.2.2
published 11 months ago
Rankings
Maintainers (1)
Dependencies
- Cython *
- MDAnalysis ==1.1.1
- h5py *
- matplotlib *
- numpy *
- pandas *
- pyyaml *
- recommonmark *
- scipy *
- sphinx *
- sphinx-markdown-tables *
- sphinx-math-dollar *
- sphinx_rtd_theme *
- x.strip *