CycPeptMPDB (Cyclic Peptide Membrane Permeability Database)
Comprehensive database of experimentally measured membrane permeability for 7,991 structurally diverse cyclic peptides from 56 publications. Covers PAMPA, Caco-2, MDCK, RRCK assays. Actively used as benchmark for ML permeability prediction in 2025-2026.
Composite
82.5
Experimental validation
Wet-lab confirmed
Stages
IND-enablingLead ID / ADMET
Modalities
peptide
Task types
permeability_predictionproperty_prediction
Size
entries: 7
cyclic_peptides: 991
publications: 56
cyclic_peptides: 991
publications: 56
License
Academic
First release
2023-01
Last updated
2024-12
Official site
Leaderboard
→ leaderboard
Dataset
Code / GitHub
→ repository
HuggingFace
→ HF
Paper
CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides · · 2023 · paper · doi:10.1021/acs.jcim.2c01573 · 45 citations
Flags
biologicspeptide_therapeuticspermeability
Experts
—
Groups
—
Hosted by
—
Related benchmarks
Rubric (7-criterion)
rigor
4
coverage
4
maintenance
4
adoption
4
quality
4
accessibility
4
industry_relevance
5
Notes
De facto standard benchmark for cyclic peptide permeability prediction. Multiple 2025-2026 papers benchmark 13+ ML methods against this dataset. Critical for beyond-rule-of-5 drug discovery. Version 1.2 updated Dec 2024.