trRosetta2

This package contains deep learning models and related scripts used by Baker group in CASP14.

Installation

Linux/Mac

1. clone the package

git clone https://github.com/RosettaCommons/trRosetta2
cd trRosetta2

2. create conda environment using one of the .yml files: casp14-baker-linux-cpu.yml, casp14-baker-linux-gpu.yml, casp14-baker-mac-cpu.yml

conda env create -f casp14-baker-linux-gpu.yml
conda activate casp14-baker

3. download network weights [1.1G]

wget https://files.ipd.uw.edu/pub/trRosetta2/weights.tar.bz2
tar xf weights.tar.bz2

4. download and install third-party software

./install_dependencies.sh

5. download sequence and structure databases

# uniclust30 [46G]
wget http://wwwuser.gwdg.de/~compbiol/uniclust/2020_06/UniRef30_2020_06_hhsuite.tar.gz
mkdir -p UniRef30_2020_06
tar xf UniRef30_2020_06_hhsuite.tar.gz -C ./UniRef30_2020_06

# structure templates [8.3G]
wget https://files.ipd.uw.edu/pub/trRosetta2/pdb100_2020Mar11.tar.gz
tar xf pdb100_2020Mar11.tar.gz

Obtain a PyRosetta licence and install the package in the newly created casp14-baker conda environment (link).

Usage

mkdir -p examples/T1078
./run_pipeline.sh example/T1078.fa example/T1078

Links

• Robetta server

References

[1] I Anishchenko, M Baek, H Park, J Dauparas, N Hiranuma, S Mansoor, I Humphrey, D Baker. Protein structure prediction guided by predicted inter-residue geometries. In: CASP14 Abstract Book, 2020

[2] H Park, M Baek, N Hiranuma, I Anishchenko, S Mansoor, J Dauparas, D Baker. Model refinement guided by an interplay between Deep-learning and Rosetta. In: CASP14 Abstract Book, 2020

[3] M Baek, I Anishchenko, H Park, I Humphrey, D Baker. Protein oligomer structure predictions guided by predicted inter-chain contacts. In: CASP14 Abstract Book, 2020