BioJava-ModFinder

BioJava-ModFinder identifies and annotates protein modifications in three-dimensional structures from the Protein Data Bank (PDB) to support structural analysis of modified residues, attachment modifications, and cross-links.

Key Features:

• Curated modification dataset: Contains over 400 types of protein modifications compiled from PDB, RESID, and PSI-MOD.
• Categorization of modifications: Classifies modifications into modified residues, attachment modifications, and cross-links.
• PDB-wide scanning: Scans all archived 3D structures in the PDB and has identified over 30,000 structures containing protein modifications.
• Detection and annotation algorithms: Implements algorithms that detect and annotate modification instances within PDB entries.
• Integration with RCSB PDB: Programmatic integration augments sequence diagrams and structure annotations within the RCSB PDB ecosystem.

Scientific Applications:

• Explore protein functionality: Maps protein modifications onto 3D structures to support analysis of their roles in protein behavior and interactions.
• Facilitate drug discovery: Identifies modification sites on proteins that can inform target selection and structure-based drug design.
• Advance structural annotation: Produces detailed modification annotations that enhance structural databases and downstream computational analyses.

Methodology:

Collects and curates modification data from PDB, RESID, and PSI-MOD. Categorizes modifications into predefined groups (modified residues, attachment modifications, cross-links). Implements algorithms that scan PDB entries to detect and annotate these modifications.