Morphology-Aware Peptide Discovery via Masked Conditional Generative Modeling

arXiv:2509.02060v4 Announce Type: replace
Abstract: Peptide self-assembly prediction offers a powerful bottom-up strategy for designing biocompatible, low-toxicity materials for large-scale synthesis in a broad range of biomedical and energy applications. However, screening the vast sequence space for categorization of aggregate morphology remains intractable. We introduce PepMorph, an end-to-end peptide discovery pipeline that generates novel sequences that are not only prone to aggregate but whose self-assembly is steered toward fibrillar or spherical morphologies by conditioning on isolated peptide descriptors that serve as morphology proxies. To this end, we compiled a new dataset by leveraging existing aggregation propensity datasets and extracting geometric and physicochemical descriptors. This dataset is then used to train a Transformer-based Conditional Variational Autoencoder with a masking mechanism, which generates novel peptides under arbitrary conditioning. After filtering to ensure design specifications and validation of generated sequences through coarse-grained molecular dynamics (CG-MD) simulations, PepMorph yielded 83% success rate under our CG-MD validation protocol and morphology criterion for the targeted class, showcasing its promise as a framework for application-driven peptide discovery.