mooninrain / trRosetta

A package to predict protein inter-residue geometries from sequence data

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trRosetta

This package is a part of trRosetta protein structure prediction protocol developed in: Improved protein structure prediction using predicted inter-residue orientations. It includes tools to predict protein inter-residue geometries from a multiple sequence alignment or a single sequence.

Contact: Ivan Anishchenko, aivan@uw.edu

Updates

trRosetta2 is now available (May 20, 2021)

Requirements

tensorflow (tested on versions 1.13 and 1.14)

Download

# download package
git clone https://github.com/mooninrain/trRosetta
cd trRosetta

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

Usage

python ./network/predict.py -m ./model2019_07 7 example/T1001.a3m example/T1001.npz example/T1001.npy

or

python ./network/predict_many.py -m ./model2019_07 7 example2/input example2/output example2/gt

Links

References

J Yang, I Anishchenko, H Park, Z Peng, S Ovchinnikov, D Baker. Improved protein structure prediction using predicted inter-residue orientations. (2020) PNAS. 117(3): 1496-1503

About

A package to predict protein inter-residue geometries from sequence data

License:MIT License


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