gjoni / trDesign

trRosetta for protein design

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

trRosetta for protein design

The package summarizes developments on the use of trRosetta structure prediction network for various protein design applications. We provide core codes for the following papers:

01. I Anishchenko, TM Chidyausiku, S Ovchinnikov, SJ Pellock, D Baker. De novo protein design by deep network hallucination. (2020) bioRxiv, doi:10.1101/2020.07.22.211482. PDF

02. C Norn, B Wicky, D Juergens, S Liu, D Kim, B Koepnick, I Anishchenko, Foldit Players, D Baker, S Ovchinnikov. Protein sequence design by explicit energy landscape optimization. (2020) bioRxiv, doi:10.1101/2020.07.23.218917. LINK

Requirements

tensorflow (tested on versions 1.13 and 1.14)

Download and installation

# download package
git clone --recursive https://github.com/gjoni/trDesign
cd trDesign

# download trRosetta network weights
wget https://files.ipd.uw.edu/pub/trRosetta/model2019_07.tar.bz2
tar xf model2019_07.tar.bz2 -C trRosetta/

# download background network weights
wget https://files.ipd.uw.edu/pub/trRosetta/bkgr2019_05.tar.bz2
mkdir -p background && tar xf bkgr2019_05.tar.bz2 -C background/

Links

About

trRosetta for protein design


Languages

Language:Jupyter Notebook 99.0%Language:Python 1.0%