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KULL-Centre / DEERpredict

Software for the prediction of DEER and PRE data from conformational ensembles.
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biophysics deer epr molecular-simulation nmr-spectroscopy

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Build Status Documentation Status DOI SWH

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:

  pip install DEERPREdict

or clone the repo:

  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

  conda create -n myenv python=3.9 pip
  conda activate myenv
  pip install -e .

Documentation

Documentation Status

Testing

Run all the tests in one go

  cd DEERpredict

  python -m pytest

or run single tests, e.g.

  cd DEERpredict

  python -m pytest tests/test_PRE.py::test_ACBP
  python -m pytest tests/test_DEER.py::test_T4L

Authors

Giulio Tesei (@gitesei)

João M Martins (@joaommartins)

Micha BA Kunze (@mbakunze)

Ramon Crehuet (@rcrehuet)

Kresten Lindorff-Larsen (@lindorff-larsen)

Article

Tesei G, Martins JM, Kunze MBA, Wang Y, Crehuet R, et al. (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