XLmap

XLmap evaluates protein structure models using chemical cross-linking mass spectrometry (XL-MS) data to score and visualize inter-residue distance constraints for model selection.

Key Features:

• Integration with XL-MS Data: Utilizes spatial information from cross-linked residues identified by XL-MS to provide proximity and distance constraints between reactive amino acids.
• Model Selection Assistance: Compares XL-MS-derived site interactions with protein structure contact maps to identify models that satisfy cross-linking constraints.
• Visualization Capabilities: Maps cross-linked sites onto protein structures to visualize conformations and contacts.
• Model Scoring and Statistical Analysis: Assesses compatibility of observed cross-links with predicted inter-residue distances and scores models based on adherence to empirical constraints.

Scientific Applications:

• Structural model evaluation: Validates and discriminates among computational protein structure models using XL-MS distance restraints.
• Model refinement and selection: Improves accuracy of structural predictions by identifying models consistent with experimental cross-link data.
• Protein dynamics and mechanism studies: Provides insights into protein conformations and dynamics through mapped cross-link restraints.
• Protein–protein interaction and complex analysis: Supports analysis of protein–protein interfaces and complex formation by locating inter-molecular cross-links.

Methodology:

Aligns experimental cross-linking data with theoretical contact maps, assesses compatibility of observed cross-links with predicted inter-residue distances, and scores models based on adherence to these empirical constraints using statistical analysis and visualization techniques.