CycPeptMPDB

CycPeptMPDB catalogs membrane permeability measurements and corresponding structural representations for cyclic peptides to support assessment of oral bioavailability and intracellular targeting in cyclic peptide drug discovery.

Key Features:

• Curated dataset: Contains information on 7,334 cyclic peptides compiled from 45 published scientific papers and two pharmaceutical patents.
• Experimentally measured permeability: Records experimentally measured membrane permeability values for each peptide.
• HDL sequence representation: Uses hierarchical editing language for macromolecules (HDL) notation to provide a uniform and unambiguous sequence representation for cyclic peptides.
• Structural annotation: Documents peptide structures alongside their measured permeability values.
• Data analysis tools: Includes comprehensive data analysis capabilities for examining peptide properties and permeability trends.
• Data visualization: Provides data visualization capabilities to explore permeability trends and patterns.

Scientific Applications:

• Oral bioavailability assessment: Support evaluation of membrane permeability as a determinant of oral bioavailability for cyclic peptides.
• Intracellular targeting: Inform design of cyclic peptides intended to target intracellular protein–protein interactions.
• Model training and benchmarking: Serve as a dataset for training and benchmarking computational models predicting membrane permeability.
• Structure–permeability analysis: Enable analysis of relationships between peptide structural features and membrane permeability.

Methodology:

Compiled a dataset of 7,334 cyclic peptides from 45 published papers and two pharmaceutical patents, recorded peptide structures and experimentally measured membrane permeability values, and represented sequences using hierarchical editing language for macromolecules (HDL) notation.