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An all-atom protein generative model.

Alexander E Chu1,2, Jinho Kim2,3, Lucy Cheng4

  • 1Biophysics Program, Stanford University, Stanford, CA 94305.

Proceedings of the National Academy of Sciences of the United States of America
|June 25, 2024

View abstract on PubMed

Summary
This summary is machine-generated.

This study introduces Protpardelle, an all-atom diffusion model for protein design. It enables simultaneous generation of protein structure and sequence, creating high-quality proteins with natural sidechain characteristics.

Keywords:
full-atom modelgenerative modelingprotein designprotein structuresidechain generation

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Area of Science:

  • Computational Biology
  • Protein Engineering
  • Artificial Intelligence in Biochemistry

Background:

  • Protein function is driven by chemical interactions, primarily involving sidechains.
  • Accurate modeling of these interactions is crucial for effective protein design.
  • Existing generative models face challenges in handling the complex, multi-state nature of proteins.

Purpose of the Study:

  • To develop an all-atom generative model for protein structure and sequence design.
  • To address the challenge of jointly modeling continuous and discrete protein properties.
  • To enable de novo protein design with high fidelity.

Main Methods:

  • Developed Protpardelle, an all-atom diffusion model for protein structure.
  • Represented all sidechain states simultaneously as a "superposition" state.
  • Integrated with sequence design methods for joint structure-sequence codesign.

    • Main Results:

    • Generated proteins exhibit high quality, diversity, and novelty.
    • Modeled sidechains accurately reproduce chemical features and behavior of natural proteins.
    • Demonstrated successful all-atom protein design and functional motif scaffolding.

    Conclusions:

    • Protpardelle offers a novel approach to all-atom protein design.
    • The model effectively codesigns protein structure and sequence.
    • This method facilitates backbone- and rotamer-free functional motif design.