ArticleJournal of chemical information and modeling2026
HELM-BERT: Topology-Aware Representations for Chemically Modified Peptides.
Article in Journal of chemical information and modeling, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Chemically modified and macrocyclic peptides are increasingly important therapeutics, yet current molecular representation models do not natively represent chemical modification and covalent topology in a unified way. Atom-level strings obscure macrocyclic connectivity, whereas protein sequence models cannot encode noncanonical residues and explicit cross-links. Here we pretrain an encoder-only transformer directly on Hierarchical Editing Language for Macromolecules (HELM) notation, which specifies monomer identity and connectivity. In this work, we show that the resulting representations achieve best mean performance in cyclic peptide membrane permeability prediction (random split
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