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

作者：Yuqian Liu, Zhongming Su, Wenzhen Yang, D Li, Jiawen Zhang, Yuning Zhang, Tao Zeng, Yong Zhang, Yuxiang Li, Guangyi Fan, Kailong Ma, Shanshan Liu, Xun Xu, Yuliang Dong, Zongan Wang · 发表于：GigaScience · 年份：2026 · DOI：10.1093/gigascience/giag076 · 被引用次数：2 · 研究领域：Nanopore and Nanochannel Transport Studies、Advanced Electron Microscopy Techniques and Applications、Genomics and Phylogenetic Studies

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.