frame2seq 0.0.7

Frame2seq for protein sequence design

Frame2seq

Official repository for Frame2seq, a structured-conditioned masked language model for protein sequence design, as described in our preprint Structure-conditioned masked language models for protein sequence design generalize beyond the native sequence space.

Colab notebook

Colab notebook for generating sequences with Frame2seq:

Setup

To use Frame2seq, install via pip:

pip install frame2seq

Usage

Sequence design

To use Frame2seq to generate sequences, you can use the design function.

from frame2seq import Frame2seqRunner

runner = Frame2seqRunner()
runner.design(pdb_file, chain_id, temperature, num_samples)

Arguments

• pdb_file: Path to PDB file.
• chain_id: Chain ID of protein.
• temperature: Sampling temperature.
• num_samples: Number of sequences to sample.
• save_neg_pll: Whether to save the per-residue negative log-likelihoods of the sampled sequences.
• verbose: Whether to print the sampled sequences and time taken for sampling.

Outputs (.fasta of sampled sequence)

>pdbid=2fra chain_id=A recovery=62.67% score=0.83 temperature=1.0
PPSSVDWRDLGCITDVLDMGGCGACWAFSAVGALEARTTQKTGELTRLSAQDLVDCAREKYGNEGCDGGRMKSSFQFIIDKNGIDSHQAYPFTASDQECLYNSKYKAATCTDYTVLPEGDEDKLREAVSNVGPVAVGIDATHPEFRNFKSGVYHDPKCTTETNHGVLVVGYGTLKGKRFYKVKTCWGTYFGEDGFIRVAKNQGNHCGISTDPSYPEM

Citing this work

@article{akpinaroglu2023structure,
  title={Structure-conditioned masked language models for protein sequence design generalize beyond the native sequence space},
  author={Akpinaroglu, Deniz and Seki, Kosuke and Guo, Amy and Zhu, Eleanor and Kelly, Mark JS and Kortemme, Tanja},
  journal={bioRxiv},
  pages={2023--12},
  year={2023},
  publisher={Cold Spring Harbor Laboratory}
}

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