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Related Experiment Video

Updated: Jun 27, 2026

Membrane Transport Processes Analyzed by a Highly Parallel Nanopore Chip System at Single Protein Resolution
11:55

Membrane Transport Processes Analyzed by a Highly Parallel Nanopore Chip System at Single Protein Resolution

Published on: August 16, 2016

NanoporeDB: A Structural Resource Of Multimeric Protein Nanopores For Single-Molecule Sensing.

Yuqian Liu1,2, Zidong Su2,3, Wenzhen Yang4

  • 1College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.

Gigascience
|June 25, 2026
PubMed
Summary
This summary is machine-generated.

NanoporeDB is a new database providing over 7,000 protein nanopore models. This structural resource expands the known nanopore repertoire, aiding biosensing and diagnostics.

Keywords:
AlphaFoldProtein nanoporeprotein structure predictionsingle-molecule sensingtransmembrane pore geometry

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Last Updated: Jun 27, 2026

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11:55

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Published on: August 16, 2016

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Area of Science:

  • Structural biology
  • Biotechnology
  • Bioinformatics

Background:

  • Protein nanopores are crucial biological gateways for biosensing and sequencing.
  • Limited experimentally resolved structures hinder the discovery and engineering of novel nanopore scaffolds.

Purpose of the Study:

  • To create a comprehensive structural resource for protein nanopores.
  • To facilitate structure-informed functional inference and advance nanopore technology.

Main Methods:

  • Utilized structure- and sequence-guided mining of large protein datasets (AlphaFold Protein Structure Database, UniRef90, MGnify90).
  • Generated high-confidence multimeric models using AlphaFold-Multimer and AlphaFold3.
  • Annotated models with predicted membrane embedding, pore geometry, and constriction profiles.

Main Results:

  • Developed NanoporeDB, an open-access resource with ~7,000 multimeric protein nanopore models.
  • Achieved a >170-fold expansion of the structurally annotated nanopore repertoire.
  • Provided an interactive web interface with 3D visualization and quantitative metrics.

Conclusions:

  • NanoporeDB is the first comprehensive structural resource for multimeric protein nanopores with membrane and pore annotations.
  • This resource serves as a gateway for advancing nanopore-based molecular sensing, diagnostics, and synthetic biology.
  • The database is publicly accessible at https://db.genomics.cn/nanopore.