End-to-end mapping of membrane transport from chemical structure to microorganisms

Membrane transport is a fundamental biological process with profound implications for pharmacology, biotechnology, and microbiology. While computational approaches have largely adopted a protein-centric perspective to annotate transportomes, inferring transport function directly from the intrinsic properties of substrates remains a major challenge. Addressing transport at the compound level enables the systematic evaluation of whether molecules undergo active transport and by which mechanisms, independent of prior transporter annotation. Here, we introduce ChemProFlow, a comprehensive computational framework that redefines transport analysis from a substrate-centric perspective. By integrating geometric deep learning with orthology-based genomic mapping, ChemProFlow predicts molecular transportability, assigns transport mechanisms according to the Transporter Classification Database, and identifies the microorganisms encoding the corresponding transport systems. We show that this integrated pipeline enables scalable, end-to-end mapping of substrate-transporter-organism relationships, with broad applications in pharmacology for anticipating drug transport, in biotechnology for guiding strain engineering, and in microbiology for dissecting substrate utilization across diverse taxa. By capturing the chemical derminants of transportabiliy, ChemProFlow generalizes to previously unseen substrates and provides a high-throughput framework for systematic exploration of molecular transport across diverse biological contexts.