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<p>Protein–protein interactions (PPIs) are important therapeutic targets but remain difficult to modulate with conventional small molecules. Peptide ligands can engage extended interfaces with high affinity and specificity, and advances in AI-enabled peptide drug design have increased the demand for curated peptide–protein interaction datasets. Here we present PPIKB, a knowledge-based data resource of peptide ligand–protein interaction, including structures and quantitative interaction measurements such as Kd, Ki or IC50. These data were manually extracted from 3,894 peer-reviewed articles, 553 public patents, and Protein Data Bank (PDB) records. The quantitative interaction module comprises 21,845 binding measurements for 2,151 protein targets, with standardized identifiers and units, peptide sequence and modification annotations, physicochemical descriptors, assay metadata, and bibliographic links. The structural module integrates 18,005 experimentally resolved protein–peptide complexes annotated with chain assignments, experimental method, resolution, and residue-level noncovalent contacts. The modules are cross-linked via shared UniProt and PDB identifiers to support retrieval of matched structure–measurement records and downstream reuse, including model training and benchmarking, similarity-based retrieval, and comparative analyses of peptide–protein interactions.</p>

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A data resource of peptide–protein interaction structures and binding affinities for peptide drug discovery

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年7月27日

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  • Ning Zhu,
  • Yanyu Ming,
  • Chengyun Zhang,
  • Sen Cao,
  • Chongyang Li,
  • Yaling Wu,
  • Jingjing Guo,
  • Hongliang Duan

摘要

Protein–protein interactions (PPIs) are important therapeutic targets but remain difficult to modulate with conventional small molecules. Peptide ligands can engage extended interfaces with high affinity and specificity, and advances in AI-enabled peptide drug design have increased the demand for curated peptide–protein interaction datasets. Here we present PPIKB, a knowledge-based data resource of peptide ligand–protein interaction, including structures and quantitative interaction measurements such as Kd, Ki or IC50. These data were manually extracted from 3,894 peer-reviewed articles, 553 public patents, and Protein Data Bank (PDB) records. The quantitative interaction module comprises 21,845 binding measurements for 2,151 protein targets, with standardized identifiers and units, peptide sequence and modification annotations, physicochemical descriptors, assay metadata, and bibliographic links. The structural module integrates 18,005 experimentally resolved protein–peptide complexes annotated with chain assignments, experimental method, resolution, and residue-level noncovalent contacts. The modules are cross-linked via shared UniProt and PDB identifiers to support retrieval of matched structure–measurement records and downstream reuse, including model training and benchmarking, similarity-based retrieval, and comparative analyses of peptide–protein interactions.