DBNAMP: A Chemically Curated Database of Noncanonical Antimicrobial Peptides with Standardized Molecular Representations

Abstract

Antimicrobial peptides (AMPs) are promising anti-infective agents, yet conventional sequence-centered resources often inadequately represent noncanonical residues, stereochemical variations, terminal modifications, cyclization, lipidation, stapling, and peptidomimetic scaffolds, limiting chemically meaningful annotation, comparison, and structure–activity relationship analysis. Here, we present DBNAMP, a manually curated and chemically explicit database of AMP-like entities containing residue-level noncanonical features, molecular-level covalent modifications, or both; it currently comprises 1,859 curated entries, including 1,421 entries with computed representative three-dimensional conformers and 129 standardized controlled-vocabulary records for noncanonical residues and peptide modifications. Among 537 source-level ambiguity-audit records, 84 remained unresolved after review, of which 82 retained at least one uppercase X character. Only one such record was included in the final release. Each DBNAMP entry integrates sequence, chemical annotation, antimicrobial activity, target organisms, physicochemical descriptors, molecular representations, structural information, and literature or patent provenance. In addition to browsing, filtering, and data download, DBNAMP enables chemically informed exploration of related peptide entities through standardized molecular representations and incorporates a lightweight SMILES-based prioritization module for preliminary ranking of candidate molecules. By bridging sequence-level peptide annotation and chemically explicit molecular representation, DBNAMP supports chemoinformatics analysis, structure–activity relationship studies, virtual screening, and computer-aided design of chemically diverse AMP candidates and is freely accessible at https://dbnamp.cn/.