PespotDB

PespotDB catalogs domain–peptide interaction data for SH2 and SH3 domains and their peptide ligands by integrating high-density peptide chip experiments and literature-derived evidence to map interactions across the human proteome.

Key Features:

• High-Density Peptide Chip Technology: Uses high-density peptide chip assays with peptides immobilized on glass surfaces to probe binding affinities of SH2 and SH3 domains.
• Extensive Interaction Data: Contains experimentally identified interactions for over 70 SH2 domains and results from testing 60 human SH3 domains against more than 9,000 poly-proline-containing peptides.
• Integration with Orthogonal Data: Integrates peptide chip data with context-specific information derived from text mining and literature curation.
• Validation and Characterization: Supports validation and characterization of interactions using pull-down assays, SPOT synthesis, and phage display experiments.
• Probabilistic Interaction Network: Combines experimental and contextual data to construct probabilistic interaction networks for SH2 domains, enabling prediction of dynamic interactions such as between SHP2 and phosphorylated tyrosines.

Scientific Applications:

• Signal Transduction Research: Provides SH2 domain–peptide interaction data relevant to studying modulation of cellular signaling pathways.
• Protein Complex Assembly Studies: Provides SH3 domain binding information for analysis of multi-protein complex assembly mediated by proline-rich motifs.
• Network Biology and Systems Biology: Enables construction and analysis of interaction networks for systems-level study of cellular interactions and pathways.

Methodology:

Applies text-mining and literature-based information extraction to annotate interactions in databases such as MINT, and integrates those annotations with peptide chip experimental results to build probabilistic interaction networks for SH2 domains.