ArticleJournal of chemical information and modeling2023
CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides.
Article in Journal of chemical information and modeling, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed, 69 citations in OpenAlex.
- Benchmarking AI-driven protocols for cyclic peptide conformer prediction and ranking.RSC medicinal chemistry · 2026Article
- MEGPNM as a multiscale edge-aware GAT network with hybrid pooling predicting permeability of non-peptidic macrocycles.Communications chemistry · 2026Article
- Similarity-Enhanced Representation Learning of Non-Canonical Amino Acids for Therapeutic Peptide Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Design of peptides with noncanonical amino acids using flow matching.Bioinformatics (Oxford, England) · 2026Article
- A decoupled alignment kernel for peptide membrane permeability predictions.Journal of cheminformatics · 2026Article
- Topical strategies for antimicrobial delivery of peptide medicines for the management of chronic wounds.Discover nano · 2026Review
- HELM-BERT: Topology-Aware Representations for Chemically Modified Peptides.Journal of chemical information and modeling · 2026Article
- PeptiVerse: A unified platform for therapeutic peptide property prediction.Nature communications · 2026Article
- Article
- Multiscale Modeling of the Bacterial Ribosome to Identify Potential Peptide Modulators and Their Allosteric Effects.Biochemistry · 2026Article
- Cyclic Peptides as Modulators of Protein-Protein Interactions: A Survival Guide from Discovery Platforms to AI-Driven Design.International journal of molecular sciences · 2026Review
- Scaling SMILES-based chemical language models for therapeutic peptide engineering.bioRxiv : the preprint server for biology · 2026Article
- Helmkit: fast and robust conversion of HELM notation to atomistic representations for large-scale macromolecular informatics.Journal of cheminformatics · 2026Article
- Design of permeability-optimized target-binding macrocyclesChemical science · 2026Article
- Revisiting ADMET prediction reliability under real-world challenges in the foundation model era.Journal of cheminformatics · 2026Article
- Contemporary data-driven innovations in peptide-based therapeutic design.Briefings in bioinformatics · 2026Review
- Predictive machine learning models for rational permeability design in de novo macrocycle engineering: a review.Journal of cheminformatics · 2026Review
- Interactions of Cyclic Peptides Ribifolin and Gramicidin S with Montmorillonite Surface by Molecular Modeling.ACS omega · 2026Article
- PEGASUS: Unlocking Polarity in Cell-Permeable Cyclic Peptides Using AI Models Built on Massively Parallel Biological Assays.Journal of medicinal chemistry · 2026Article
- The Biggest Challenge for Prediction of Membrane Permeability of Cyclic Peptides: Scarce Data Availability.Journal of medicinal chemistry · 2026Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recently, cyclic peptides have been considered breakthrough drugs because they can interact with "undruggable" targets such as intracellular protein-protein interactions. Membrane permeability is an essential indicator of oral bioavailability and intracellular targeting, and the development of membrane-permeable peptides is a bottleneck in cyclic peptide drug discovery. Although many experimental data on membrane permeability of cyclic peptides have been reported, a comprehensive database is not yet available. A comprehensive membrane permeability database is essential for developing computational methods for cyclic peptide drug design. In this study, we constructed CycPeptMPDB, the first web-accessible database of cyclic peptide membrane permeability. We collected information on a total of 7334 cyclic peptides, including the structure and experimentally measured membrane permeability, from 45 published papers and 2 patents from pharmaceutical companies. To unambiguously represent cyclic peptides larger than small molecules, we used the hierarchical editing language for macromolecules notation to generate a uniform sequence representation of peptides. In addition to data storage, CycPeptMPDB provides several supporting functions such as online data visualization, data analysis, and downloading. CycPeptMPDB is expected to be a valuable platform to support membrane permeability research on cyclic peptides. CycPeptMPDB can be freely accessed at http://cycpeptmpdb.com.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.