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<p>Cyclic peptides are increasingly explored as modulators of difficult-to-drug targets and protein-protein interactions, yet structure-centered resources with standardized, computable annotations remain limited. Here we present HighDB, a curated database of experimentally resolved cyclic peptide structures collected from the Protein Data Bank and related literature. The current release contains 2,504 entries annotated at the PDB-chain level and harmonized across cyclization type, ring number, overall secondary structure, peptide naturalness, and complex context. HighDB combines keyword retrieval, multidimensional filtering, sequence-similarity search, and interactive three-dimensional visualization to support comparative structural analysis, dataset construction, template retrieval, and design-oriented exploration of cyclic peptide space. In addition to database development, we provide a unified annotation framework for topological and conformational descriptors and compare HighDB with representative cyclic peptide resources, showing broader annotation coverage and the largest collection of experimentally resolved cyclic peptide structures among the databases examined. HighDB is freely accessible for academic use at <a href="http://highdb.duanlab.ac/">http://highdb.duanlab.ac/</a>.</p>

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HighDB: a structure-annotated cyclic peptide database for comparative analysis, template retrieval, and design-oriented applications

  • 期刊论文

  • 发表日期：

    2026年7月14日

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  • Yiqi Xu,
  • Ning Zhu,
  • Tianfeng Shang,
  • Shiyi Yao,
  • Hongliang Duan

摘要

Cyclic peptides are increasingly explored as modulators of difficult-to-drug targets and protein-protein interactions, yet structure-centered resources with standardized, computable annotations remain limited. Here we present HighDB, a curated database of experimentally resolved cyclic peptide structures collected from the Protein Data Bank and related literature. The current release contains 2,504 entries annotated at the PDB-chain level and harmonized across cyclization type, ring number, overall secondary structure, peptide naturalness, and complex context. HighDB combines keyword retrieval, multidimensional filtering, sequence-similarity search, and interactive three-dimensional visualization to support comparative structural analysis, dataset construction, template retrieval, and design-oriented exploration of cyclic peptide space. In addition to database development, we provide a unified annotation framework for topological and conformational descriptors and compare HighDB with representative cyclic peptide resources, showing broader annotation coverage and the largest collection of experimentally resolved cyclic peptide structures among the databases examined. HighDB is freely accessible for academic use at http://highdb.duanlab.ac/.