CPPsite3: An updated large repository of experimentally validated cell- penetrating peptides

CPPsite3 is the most recent and comprehensive update to the CPPsite series, representing a major expansion in the availability of experimentally validated cell-penetrating peptides (CPPs). This repository builds upon its predecessors, CPPsite and CPPsite2, and currently houses 6,788 entries representing 4,285 unique CPPs[cite: 4]. It serves as a vital resource for the drug delivery research community, particularly for those utilizing artificial intelligence and machine learning to discover novel peptides.

Web Server: https://webs.iiitd.edu.in/raghava/cppsite3/

Citation

Bajiya, N., Najrin, S., Kumar, P., Choudhury, S., Tomer, R., & Raghava, G. P. S. (2025). CPPsite3: An updated large repository of experimentally validated cell-penetrating peptides. Drug Discovery Today, Volume 30, Number 8. https://doi.org/10.1016/j.drudis.2025.104421

About the Database

CPPs are short peptides (fewer than 30 amino acids) capable of crossing lipophilic membrane barriers to deliver various impermeable cargoes—such as drugs, proteins, and nucleic acids—into cells. CPPsite3 was developed to centralize the tremendous growth of CPP data reported in the last nine years, as previous versions only contained information up to 2015.

Data Sourcing: Relevant research articles were manually extracted from PubMed for the period between July 2015 and April 2024.

Expansion: The update adds 4,933 new entries (from 1,471 unique PubMed IDs) to the existing 1,855 records from older versions, representing a 3.14-fold increase in data.