GitHub repo for RoseTTAFold2
Update May 16, 2024:
-cyclize
for prediction of cyclic peptidesUpdate Apr 12, 2024:
Clone the package
git clone https://github.com/uw-ipd/RoseTTAFold2.git
cd RoseTTAFold2
Create conda environment
# create conda environment for RoseTTAFold2
conda env create -f RF2-linux.yml
You also need to install NVIDIA's SE(3)-Transformer (please use SE3Transformer in this repo to install).
conda activate RF2
cd SE3Transformer
pip install --no-cache-dir -r requirements.txt
python setup.py install
cd ..
Download pre-trained weights under network directory
cd network
wget https://files.ipd.uw.edu/dimaio/RF2_jan24.tgz
tar xvfz RF2_jan24.tgz
cd ..
Download sequence and structure databases
# uniref30 [46G]
wget http://wwwuser.gwdg.de/~compbiol/uniclust/2020_06/UniRef30_2020_06_hhsuite.tar.gz
mkdir -p UniRef30_2020_06
tar xfz UniRef30_2020_06_hhsuite.tar.gz -C ./UniRef30_2020_06
wget https://bfd.mmseqs.com/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz mkdir -p bfd tar xfz bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz -C ./bfd
wget https://files.ipd.uw.edu/pub/RoseTTAFold/pdb100_2021Mar03.tar.gz tar xfz pdb100_2021Mar03.tar.gz
## Examples
Prepare to run
conda activate RF2 cd example
### Example 1: predicting the structure of a monomer
../run_RF2.sh rcsb_pdb_7UGF.fasta -o 7UGF
### Example 2: predicting the structure of a heterodimer with paired MSA
../run_RF2.sh rcsb_pdb_8HBN.fasta --pair -o 8HBN
### Example 3: predicting the structure of a heterotrimer with paired MSA
../run_RF2.sh rcsb_pdb_7ZLR.fasta --pair -o 7ZLR
### Example 4: predicting the structure of a C6-symmetric homodimer
../run_RF2.sh rcsb_pdb_7YTB.fasta --symm C6 -o 7YTB
### Example 5: predicting the structure of a C3-symmetric heterodimer (A<sub>3</sub>B<sub>3</sub> complex) with paired MSA
../run_RF2.sh rcsb_pdb_7LAW.fasta --symm C3 --pair -o 7LAW
### Expected outputs
Predictions will be output to the folder 1XXX/models/model_final.pdb. B-factors show the predicted LDDT.
A json file and .npz file give additional accuracy information.
## Additional information
The script `run_RF2.sh` has a few extra options that may be useful for runs:
Usage: run_RF2.sh [-o|--outdir name] [-s|--symm symmgroup] [-p|--pair] [-h|--hhpred] input1.fasta ... inputN.fasta Options: -o|--outdir name: Write to this output directory -s|--symm symmgroup (BETA): run with the specified spacegroup. Understands Cn, Dn, T, I, O (with n an integer). -p|--pair: If more than one chain is provided, pair MSAs based on taxonomy ID. -h|--hhpred: Run hhpred to generate templates