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Updated: Jun 29, 2026

Mapping Dysfunctional Protein-Protein Interactions in Disease

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

PMAP: databases for analyzing proteolytic events and pathways.

Yoshinobu Igarashi¹, Emily Heureux, Kutbuddin S Doctor

¹The Center on Proteolytic Pathways, The Cancer Research Center and The Inflammatory and Infectious Disease Center, The Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.

Nucleic Acids Research

|October 10, 2008

Summary

This summary is machine-generated.

The Proteolysis MAP (PMAP) is a website aiding scientists in understanding proteolytic networks. It integrates five databases for comprehensive analysis of proteases, substrates, and pathways.

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Area of Science:

Biochemistry
Bioinformatics
Molecular Biology

Background:

Proteolytic pathways are crucial in biological processes.
Understanding these networks requires integrated data resources.
Existing tools lack comprehensive integration for proteolysis research.

Purpose of the Study:

To introduce the Proteolysis MAP (PMAP) as a unified platform for studying proteolytic networks.
To facilitate reasoning about protease function, substrate interactions, and pathway dynamics.
To provide a user-friendly environment for accessing and analyzing proteolysis-related data.

Main Methods:

Development of five interconnected databases: ProteaseDB, SubstrateDB, CutDB, ProfileDB, and PathwayDB.
Implementation of an automated annotation pipeline for dynamic 'Molecule Pages'.
Integration of community-annotated data on proteolytic events and substrate specificity.
Inclusion of a Protease Toolkit for data analysis.

Main Results:

PMAP offers a comprehensive resource with over 5000 documented proteolytic events.
Dynamic modeling capabilities for known and hypothetical proteolytic pathways.
Detailed information on protease substrate recognition specificity.
A centralized environment for exploring protease and substrate data.

Conclusions:

PMAP enhances the scientific community's ability to understand and reason about proteolytic networks.
The integrated databases and tools foster deeper insights into proteolysis.
PMAP serves as a valuable resource for both fundamental research and pathway analysis.