prospr 0.2a2

A toolbox for protein folding with Python.

Prospr: The Protein Structure Prediction Toolbox

Creator: Okke van Eck

This project is a universal toolbox for protein structure prediction within the HP-model. It will contain a datastructure for creating own algorithms, pre-created algorithms, datasets and visualization functions. Besides folding proteins, this package will also make it possible to determine the relative hardness of a protein for an algorithm. This allows for a fair comparison across the different algorithms.

So far, only square lattices are supported in n-dimensions. The amino acids can only be placed in the corners of the squares and have to be one unit away from the previously placed amino acid.

Installation guide

This package can simply be installed via pip by running:

pip install prospr

Archives

All the C++ core files and datasets are also available as compressed archives. See the subsections below for direct links.

C++ core

All the core code which prospr runs on, is available as a compressed archive. The folder archives contains a .zip and a .tar.gz archive.

Datasets

The complete collection of datasets is available as a compressed archive in the archives folder. It is available as a .zip and a .tar.tz archive.

Example usage

Work in progress

Future work

This toolbox could be used for other protein folding problems within discrete models. It would be a great extension to support different models by creating a modular amino acid.

Changelog

Work in progress

License

The used license is the GNU LESSER GENERAL PUBLIC LICENSE. A copy can be found in the LICENSE file on GitHub.