RaptorX-Single

Single-sequence protein structure prediction by integrating protein language models

Environment

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b
conda env create -f environment.yml
conda activate RaptorXSingle

Code

git clone https://github.com/AndersJing/RaptorX-Single.git
cd RaptorX-Single/

Parameter

Download the following parameter files as needed, you can save these files at params/ folder.

PLM (protein language model) model parameters

• esm1b_t33_650M_UR50S.pt

  wget -P params/ https://dl.fbaipublicfiles.com/fair-esm/models/esm1b_t33_650M_UR50S.pt
  

• esm1v_t33_650M_UR90S_1.pt

  wget -P params/ https://dl.fbaipublicfiles.com/fair-esm/models/esm1v_t33_650M_UR90S_1.pt
  

• prot_t5_xl_uniref50

  wget -P params/ https://zenodo.org/record/4644188/files/prot_t5_xl_uniref50.zip
  

Parameters of RaptorX-Single

Please find the parameters at:

Parameters for general protein structure prediction

• RaptorX-Single-ESM1b.pt: wget -P params/ https://zenodo.org/records/7351378/files/RaptorX-Single-ESM1b.pt
• RaptorX-Single-ESM1v.pt: wget -P params/ https://zenodo.org/records/7351378/files/RaptorX-Single-ESM1v.pt
• RaptorX-Single-ProtTrans.pt: wget -P params/ https://zenodo.org/records/7351378/files/RaptorX-Single-ProtTrans.pt
• RaptorX-Single-ESM1b-ESM1v-ProtTrans.pt: wget -P params/ https://zenodo.org/records/7351378/files/RaptorX-Single-ESM1b-ESM1v-ProtTrans.pt

Parameters for antibody structure prediction

• RaptorX-Single-ESM1b-Ab.pt: wget -P params/ https://zenodo.org/records/7351378/files/RaptorX-Single-ESM1b-Ab.pt
• RaptorX-Single-ESM1v-Ab.pt: wget -P params/ https://zenodo.org/records/7351378/files/RaptorX-Single-ESM1v-Ab.pt
• RaptorX-Single-ProtTrans-Ab.pt: wget -P params/ https://zenodo.org/records/7351378/files/RaptorX-Single-ProtTrans-Ab.pt
• RaptorX-Single-ESM1b-ESM1v-ProtTrans-Ab.pt: wget -P params/ https://zenodo.org/records/7351378/files/RaptorX-Single-ESM1b-ESM1v-ProtTrans-Ab.pt

Usage

pred.py [-h] [--out_dir OUT_DIR] [--plm_param_dir PLM_PARAM_DIR]
               [--device_id DEVICE_ID] [--n_cycle N_CYCLE]
               [--n_worker N_WORKER]
               fasta_path param

positional arguments:
  fasta_path            fasta file or dir.
  param                 param file path.

optional arguments:
  --out_dir             output dir. (default: 'output/')
  --plm_param_dir       param path for PLM models (ESM1b, ESM1v and ProtTrans). (default: 'params/')
  --device_id           device id (-1 for CPU, >=0 for GPU). (default: -1)
  --n_cycle             cycle time. (default: 4)
  --n_worker            DataLoader num_workers. (default: 0)

Runnning

CPU

python pred.py example/seq/ params/RaptorX-Single-ESM1b.pt --out_dir=example/out/

GPU (GPU 0 as example)

python pred.py example/seq/ params/RaptorX-Single-ESM1b.pt --out_dir=example/out/ --device_id=0

Benchmark

The benchmark target lists are saved at benchmark/.

Aknowledgements

• https://github.com/facebookresearch/esm
• https://github.com/agemagician/ProtTrans

Reference

Jing, X., Wu, F., Luo, X., & Xu, J. (2024). Single-sequence protein structure prediction by integrating protein language models. Proceedings of the National Academy of Sciences, 121(13), e2308788121. Link

Jing, X., Wu, F., Luo, X., & Xu, J. (2023). RaptorX-Single: single-sequence protein structure prediction by integrating protein language models. bioRxiv, 2023-04. Link

Contact

Xiaoyang Jing: xyjing@ttic.edu