A curated reference database of membrane-permeability annotations for biological dyes

Fluorescent and chromogenic dyes are widely used for cellular labelling, imaging and functional assays, yet information on their membrane permeability remains fragmented and inconsistently documented across the literature and existing chemical resources. To address this gap, we present DyePermDB, a curated dataset of 251 biologically relevant dyes with standard chemical identifiers, literature-supported membrane-permeability annotations and standardised structural information. DyePermDB adopts a two-level annotation framework consisting of an intrinsic membrane-permeability status (Permeable or Impermeable) and a permeability-dependency context that distinguishes autonomous live-cell permeability, physicochemical-condition-dependent permeability, mediated or damage-dependent intracellular access and strict live-cell impermeability. To improve interpretability and reuse, the database records structured annotation fields describing chemical form, evidence context, localisation targets, evidence directness and condition-specific information. Chemical structures were standardised and quality-controlled through an RDKit-based workflow, with structure-quality metadata introduced to support transparent filtering and downstream cheminformatics analyses. The resource is organised into four linked datasets comprising core permeability annotations, structure-validation records, supplementary annotations and external cross-references. Exploratory FP4 fingerprint analyses provided technical validation of an internal classification signal within the curated annotations. By integrating traceable permeability evidence, standardised structures and explicit quality-control information, DyePermDB provides a reusable resource for dye-annotation review, structure-quality assessment and exploratory computational studies of membrane permeability.