Welcome to HighDB

Browse and visualize 3D structures of cyclic peptides with diverse cyclization topologies and secondary structures.

Examples: 1AB1 human X-RAY DIFFRACTION
Total entries
2504
Natural
1809
Non-natural
695

About us

HighDB is a structure-centric knowledge base and web platform for cyclic peptides with experimentally determined 3D structures curated from the Protein Data Bank (PDB). It aims to provide a standardized, searchable, and reusable structural resource for researchers working on cyclic peptides, macrocycles, and peptide–protein interactions.

The core dataset consists of PDB-derived cyclic peptide entries with verified structural evidence. For each entry, HighDB provides curated structural metadata and unified annotations, including:

  • Cyclization topology (e.g., head-to-tail, disulfide, side-chain cyclization, and their combinations)
  • Ring number (1/2/3/4/5–7, when applicable)
  • Secondary structure (e.g., α-helix, β-sheet, coil, mixed; derived via standardized workflows)
  • Experimental details (method such as X-ray/NMR/EM, release date, etc.)
  • References and basic entry-level information for traceability

To facilitate practical use, HighDB offers an interactive interface for browsing, searching, and filtering cyclic peptides by structural features (ring number, cyclization type, secondary structure), organism/source category, experimental method, and other metadata. The platform also supports structure visualization and data download to enable downstream computational analysis, benchmarking, and AI-driven peptide design.

HighDB is designed as a reproducible structural snapshot derived from public PDB records, with clear data provenance and consistent annotations, providing a reliable foundation for structure–function exploration and structure-guided peptide engineering.