WebMetabase

WebMetabase analyzes peptide substrates and predicts protease cleavage sites to support the design of peptides with reduced proteolytic degradation.

Key Features:

• Data Integration: Integrates liquid chromatography–mass spectrometry (LC-MS) experimental data and external public datasets such as the MEROPS database.
• Chemically Aware Representation: Represents each peptide substrate as a sequence of structural blocks (SBs) connected by amide bonds and supports natural and unnatural residues.
• Pharmacophoric and Physicochemical Characterization: Describes each SB by pharmacophoric features and physicochemical properties.
• Similarity Scoring: Computes a similarity score quantifying likeness between any given SB and others within the database.
• Frequency Analysis of Cleavage Sites: Performs frequency analysis on amide bonds based on the similarity of participating SBs to identify frequent cleavage sites.

Scientific Applications:

• Drug Design: Predicts protease cleavage sites to guide modifications that increase peptide stability.
• Protease Interaction Studies: Provides insights into interactions between SBs and proteases to inform inhibitor design or residue modification.
• Comparative Analysis: Enables comparison of structural features across peptides to identify patterns of cleavage susceptibility.

Methodology:

Integrates LC-MS experimental and public datasets (including MEROPS); represents peptides as sequences of structural blocks (SBs) connected by amide bonds; characterizes SBs by pharmacophoric and physicochemical properties; computes similarity scores between SBs; performs frequency analysis on amide bonds based on SB similarity to identify frequent cleavage sites.