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trRosetta2

★ 123 Open GitHub ↗

Repository for publicly available deep learning models developed in Rosetta community

// repository documentation

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# *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](https://els2.comotion.uw.edu/product/pyrosetta) and install the package in the newly created `casp14-baker` conda environment ([link](http://www.pyrosetta.org/dow)).

## Usage

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

## Links

* [Robetta server](https://robetta.bakerlab.org/)

## 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](https://predictioncenter.org/casp14/doc/CASP14_Abstracts.pdf)

[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](https://predictioncenter.org/casp14/doc/CASP14_Abstracts.pdf)

[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](https://predictioncenter.org/casp14/doc/CASP14_Abstracts.pdf)

trRosetta2

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