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ProtGPT2 is a deep unsupervised language model for protein design.

Noelia Ferruz1,2, Steffen Schmidt3, Birte Höcker4

  • 1Department of Biochemistry, University of Bayreuth, Bayreuth, Germany. noelia.ferruz-capapey@uni-bayreuth.de.

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|July 27, 2022
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Summary

ProtGPT2, a novel language model, generates de novo protein sequences that mimic natural ones. These AI-designed proteins exhibit natural characteristics and explore uncharted protein space, offering potential for environmental and biomedical applications.

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Area of Science:

  • Computational biology
  • Protein engineering
  • Artificial intelligence in life sciences

Background:

  • Protein design seeks to create novel proteins for specific environmental and biomedical applications.
  • Advancements in Transformer-based language models have demonstrated human-like text generation capabilities.

Purpose of the Study:

  • To develop ProtGPT2, a language model for generating de novo protein sequences.
  • To assess if generated sequences adhere to natural protein principles and explore novel protein space.

Main Methods:

  • Trained a Transformer-based language model (ProtGPT2) on the protein sequence space.
  • Analyzed generated sequences for natural amino acid propensities and globular characteristics using disorder predictions.
  • Performed sensitive sequence searches and similarity network analysis against protein databases.
  • Utilized AlphaFold for structural prediction of generated protein sequences.

Main Results:

  • ProtGPT2 generates de novo protein sequences that follow natural protein principles, exhibiting natural amino acid propensities.
  • 88% of ProtGPT2-generated proteins are predicted to be globular, similar to natural proteins.
  • Generated sequences are distantly related to known proteins, indicating exploration of novel protein space.
  • AlphaFold predictions reveal well-folded, non-idealized structures with unique topologies not present in current databases.

Conclusions:

  • ProtGPT2 successfully generates novel protein sequences with natural characteristics, expanding the known protein space.
  • The model's ability to produce unique structures suggests potential for new protein functionalities.
  • ProtGPT2 offers a rapid and accessible tool for advancing protein design.