XLinkDB

XLinkDB stores and visualizes protein interaction topologies derived from cross-linking mass spectrometry (XL-MS) data to support analysis of intra- and intermolecular cross-links and quantitative changes in interactomes.

Key Features:

• Data Storage: Archives cross-linked peptide data from XL-MS experiments including intra- and intermolecular protein interaction information across organelles, cells, tissues, and organs.
• Quantitative Analysis: Handles quantitative XL-MS data to detect interactome changes resulting from environmental, phenotypic, pharmacological, or genetic perturbations.
• 3D Visualization: Provides three-dimensional visualization of multiple quantitative interactome datasets across time points or perturbation levels.
• Integration (Release 3.0): Incorporates advanced informatics capabilities in release 3.0 to support analysis and interpretation of cross-linked peptide databases for structural studies.

Scientific Applications:

• Protein Structural Studies: Enables 3D visualization of protein interactions to inform structural biology and the architecture of protein complexes.
• Dynamic Interactome Analysis: Facilitates study of temporal and perturbation-driven changes in protein interaction networks.
• Pharmacological and Genetic Research: Supports analysis of how drugs or genetic modifications alter protein interactions for drug discovery and genetic studies.

Methodology:

Leverages cross-linking mass spectrometry (XL-MS) to detect intra- and intermolecular covalent cross-links between amino acids and employs quantitative XL-MS measurements for three-dimensional visualization of interaction changes.