PepX

PepX compiles an exhaustive, unbiased dataset of protein-peptide complexes from the Protein Data Bank (PDB) and provides structural annotations to support structural analysis and peptide design.

Key Features:

• Exhaustive Dataset: Compiles all available protein-peptide complexes from the PDB including peptides up to 35 residues, resulting in 505 unique protein-peptide interface clusters derived from 1431 complexes.
• Unbiased Clustering: Employs clustering based on binding interfaces rather than sequence homology to capture structurally diverse protein-peptide interactions.
• Thorough Annotation: Annotates each complex with biological and structural information.
• Facilitation of Peptide Design: Annotates peptides with naturally occurring backbone variations using fragment clusters from the BriX database.

Scientific Applications:

• Drug Discovery: Supports design and evaluation of peptide-based therapeutics targeting peptide-mediated interactions.
• Molecular Modeling: Provides a structurally diverse dataset for modeling, docking, and interface analysis of protein-peptide complexes.
• Signaling and Regulatory Network Analysis: Enables structural studies of protein-peptide interactions prevalent in cellular signaling and regulatory networks.

Methodology:

Data compiled from the Protein Data Bank (PDB); clustering performed on binding interfaces rather than sequence homology; peptide backbone variations annotated using BriX fragment clusters.