colide's Introduction

CoLiDe: Combinatorial Library Design tool for probing protein sequence space

This code repository includes the tool from the published study Link, PDF:

CoLiDe: Combinatorial Library Design tool for probing protein sequence space
Tretyachenko V, Voráček V, Souček R, Fujishima K, and Hlouchová K.
Bioinformatics 2020

The source code is released under the MIT License. See the License file for details.

Usage

on the first use download and install miniconda 3.x from https://docs.conda.io/en/latest/miniconda.html

open Anaconda prompt and run the command inside quotation marks "cd xxx", where xxx is the path to the directory with CoLiDe on first use run command inside quotation marks "conda install --file requirements.txt"
run the command inside quotation marks "python gui.py"

Documentation

A short version of a documentation follows. For the full documentation, follow this link.

Contact

The software was developed in the Klara Hlouchova Research Group, see http://khlab.org/.

For any question, you can contact [email protected]

Citation

If you use this codebase or any part of it for a publication, please cite:

@article{tretyachenko2020colide,
  title={CoLiDe: Combinatorial Library Design tool for probing protein sequence space},
  author={Tretyachenko, Vyacheslav and Vor{\'a}{\v{c}}ek, V{\'a}clav and Sou{\v{c}}ek, Radko and Fujishima, Kosuke and Hlouchov{\'a}, Kl{\'a}ra},
  journal={Bioinformatics},
  year={2020}
  doi = {10.1093/bioinformatics/btaa804},

}

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