RF2

GitHub repo for RoseTTAFold2

Update May 16, 2024:

• Fixes for training
• New option -cyclize for prediction of cyclic peptides

Update Apr 12, 2024:

• Updated config file
• Better memory efficiency during inference
• Symmetry bugfix

Installation

1. Clone the package

   git clone https://github.com/uw-ipd/RoseTTAFold2.git
   cd RoseTTAFold2

2. 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 ..

3. 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 ..

4. 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

BFD [272G]

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

structure templates (including _a3m.ffdata, _a3m.ffindex)

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