PPIKB: A Comprehensive Knowledge Base and Analysis Platform for Protein Peptide Interactions Based on Literature and Patents

Abstract

Protein-protein interactions (PPIs) underpin a multitude of fundamental biological processes and represent critical therapeutic targets. Peptide compounds--owing to their structural flexibility, high target specificity, and the combined advantages of small molecules and biologics--have emerged as powerful modulators of these interactions. However, the exponential growth of scientific publications and patent filings poses a significant challenge for the systematic integration of protein-peptide interaction (PPepI) data. To address this, we implemented a high-throughput extraction pipeline powered by large language models (LLMs) to harvest affinity data from both research articles and patents, followed by rigorous manual curation. Applying this approach to 4,241 research papers and 483 patents published between 1972 and 2025, we compiled 21,760 manually validated quantitative affinity entries encompassing 2,013 unique protein targets derived from human, mouse, rat, viral, bacterial, and other species. In parallel, we consolidated 18,005 structural entries of protein-peptide complexes from the Protein Data Bank and associated literature. Leveraging these comprehensive datasets, we developed PPIKB, a user-friendly database and analysis platform that enables efficient querying, visualization, and in-depth analysis of protein-peptide interactions. PPIKB also provides a suite of tools tailored to facilitate peptide-based drug discovery, protein engineering, and systems-level biological research. By combining state-of-the-art text-mining technologies with expert validation, PPIKB sets a new standard for accessibility and utility in the field of protein-peptide interaction data resources. Access PPIKB at: https://ppikb.duanlab.ac