NanoporeDB: a structural resource of multimeric protein nanopores for single-molecule sensing.

Abstract

Background: Protein nanopores are essential molecular gateways in biology and have inspired transformative technologies in biosensing and single-molecule sequencing. However, the discovery and engineering of novel nanopore scaffolds remains limited due to the scarcity of experimentally resolved pore structures.

Results: Here, we present NanoporeDB, an open-access structural resource comprising about 7,000 high-confidence multimeric models across 4 representative pore types. Using a structure- and sequence-guided mining strategy, we identified candidate nanopores from large protein datasets, including the AlphaFold Protein Structure Database, UniRef90, and MGnify90, and generated high-confidence multimeric models using AlphaFold-Multimer and AlphaFold3. Collectively, these models represent a >170-fold expansion of the structurally annotated nanopore repertoire. Each model is further annotated with predicted membrane embedding, pore geometry, and constriction profiles, enabling structure-informed functional inference. NanoporeDB features an interactive web interface with 3D visualization and quantitative metrics.

Conclusions: NanoporeDB provides the first comprehensive structural resource of multimeric protein nanopores with explicit membrane and pore annotations. This resource provides a structural gateway for advancing nanopore-based molecular sensing, precision diagnostics, and synthetic biology. NanoporeDB is publicly available at https://db.genomics.cn/nanopore.