FRETpredict 0.1.0

A package for FRET Efficiency prediction of protein structures and trajectories, based on the Rotamer Library Approach (RLA). Can be installed with pip.

FRETpredict

Overview

A package for FRET Efficiency prediction of protein structures and trajectories, based on the Rotamer Library Approach (RLA).

Installation

To install FRETpredict, use the PyPI package:

  pip install FRETpredict

or clone the repo and install locally:

  git clone https://github.com/KULL-Centre/FRETpredict.git
  cd FRETpredict

  pip install -e . 

The software requires Python 3.6+.

Testing

  pip install pytest
  git clone https://github.com/KULL-Centre/FRETpredict.git
  cd tests

  pytest

Code Example

import MDAnalysis
from FRET import FRETpredict

# Create a MDAnalysis.Universe object for the protein structure.
u = MDAnalysis.Universe('test_systems/Hsp90/openHsp90.pdb')

# Create instance of the FRETpredict class
FRET = FRETpredict(protein=u, residues=[452, 637], chains=['A', 'B'], temperature=293, 
                   fixed_R0=True, r0=6.3, electrostatic=True,
                   libname_1='AlexaFluor 594 C1R cutoff30',
                   libname_2='AlexaFluor 568 C1R cutoff30', 
                   output_prefix='E30_594_568')

# Run FRET efficiency calculations.
FRET.run()

Tutorials

• Tutorial_FRETpredict_Hsp90 : Jupyter Notebook with simple tutorials on how to use the code on the Hsp90 system.

• Generate new rotamer libraries : Jupyter Notebook on how to create and add new rotamer libraries.

Structure

FRETpredict/
├─ FRETpredict/
│  ├─ lib/
│  │  ├─ R0/
│  ├─ test_systems/
│  │  ├─ Hsp90/
│  ├─ tutorials/
│  │  ├─ genLIB/
│  │  ├─ test/
│  │  ├─ Tutorial_FRETpredict_Hsp90.ipynb
│  │  ├─ Tutorial_generate_new_rotamer_libraries.ipynb
│  ├─ FRET.py
│  ├─ lennardjones.py
│  ├─ libraries.py
│  ├─ R0_calculation.py
│  ├─ rotamer_libraries.py
│  ├─ utils.py
│  ├─ __init__.py
├─ tests/
|  ├─ test_Hsp90.py
├─ LICENSE
├─ README.md
├─ setup.py

Contributors

Daniele Montepietra (@Monte95)

Giulio Tesei (@gitesei)

João M Martins (@joaommartins)

Micha BA Kunze (@mbakunze)

Ramon Crehuet (@rcrehuet)

Kresten Lindorff-Larsen (@lindorff-larsen)