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Rethinking peptide developability with sequence-only models: interpretable screening of microplastic-binding peptides
Guangyao Chen1,2, Fengqi You1,2,3
1College of Engineering, Cornell University Ithaca NY 14853 USA fengqi.you@cornell.edu.
Chemical Science
|June 3, 2026
Summary
This study introduces gated query pooling (GQP) for accurate peptide developability screening using only sequence data. GQP effectively predicts and mitigates risks like hemolysis and poor solubility in microplastic-targeting peptides.
Area of Science:
- Biotechnology
- Computational Biology
- Materials Science
Background:
- Designing peptides for microplastic targeting faces multi-objective challenges, balancing adsorption with developability risks like hemolysis and poor solubility.
- Current methods often struggle to accurately predict these risks from sequence alone.
Purpose of the Study:
- To develop a sequence-only method for accurate peptide developability screening.
- To introduce and validate a novel approach, gated query pooling (GQP), for predicting peptide developability.
- To establish testable design rules for peptide development.
Main Methods:
- Introduced gated query pooling (GQP), a backbone-agnostic method using query vectors to extract signals from protein language model embeddings.
- Evaluated GQP's accuracy on hemolysis, non-fouling, and solubility prediction using a consistent protocol.
- Integrated GQP with microplastic-binding affinity scores and molecular dynamics for multi-objective prioritization.
Main Results:
- GQP achieved high accuracy in predicting peptide developability: 91.09% for hemolysis, 86.30% for non-fouling, and 75.56% for solubility.
- GQP outperformed sequence-only and AlphaFold-augmented baselines.
- Attention diagnostics and counterfactual substitutions provided residue-level design insights.
Conclusions:
- Accurate peptide developability screening is achievable from sequence alone using GQP.
- Non-fouling properties emerged as a key bottleneck in peptide design for microplastic applications.
- The integrated approach supports scalable prioritization of microplastic-binding peptides.
