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AntiFold: improved structure-based antibody design using inverse folding.

Magnus Haraldson Høie1, Alissa M Hummer2, Tobias H Olsen2

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AntiFold, a new antibody-specific inverse folding model, enhances antibody design by maintaining structural integrity. It improves sequence recovery and predicts antigen binding affinity, aiding in antibody optimization.

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Area of Science:

  • * Computational biology
  • * Protein engineering
  • * Immunology

Background:

  • * Antibody design and optimization necessitate balancing multiple properties.
  • * Protein inverse folding models generate diverse sequences for a single structure, preserving structural integrity.
  • * Existing inverse folding tools have limitations in antibody-specific applications.

Purpose of the Study:

  • * To introduce AntiFold, an antibody-specific inverse folding model.
  • * To evaluate AntiFold's performance in sequence recovery and structural similarity.
  • * To assess AntiFold's capability in predicting antibody-antigen binding affinity.

Main Methods:

  • * Fine-tuning the ESM-IF1 model on solved and predicted antibody structures.
  • * Evaluating sequence recovery in complementarity-determining regions (CDRs).
  • * Assessing structural similarity between designed and solved antibody structures.
  • * Zero-shot prediction of antibody-antigen binding affinity.

Main Results:

  • * AntiFold surpasses existing inverse folding tools in sequence recovery across CDRs.
  • * Designed sequences exhibit high structural similarity to their solved counterparts.
  • * AntiFold demonstrates stronger correlations in predicting antibody-antigen binding affinity.
  • * The model assigns low probabilities to mutations that disrupt antigen binding.

Conclusions:

  • * AntiFold is a promising tool for antibody design and optimization.
  • * It effectively maintains structural integrity while improving sequence recovery.
  • * The model aids in predicting and guiding antibody-antigen binding affinity.
  • * AntiFold synergizes with protein language models for enhanced antibody engineering.