Xwalk

Xwalk computes solvent-accessible surface distances (SASD) between chemically cross-linked amino acids on existing protein structures to predict and validate chemical cross-links and generate distance restraints for structural modeling informed by mass spectrometry-based localization.

Key Features:

• Prediction and Validation: Predicts and validates chemical cross-links on protein structures using mass spectrometry-based localization of cross-linked amino acids.
• Non-linear Distance Calculation: Calculates non-linear distances that mimic cross-linker flexibility and path non-linearity on protein surfaces.
• Solvent Accessible Surface Distance (SASD): Computes the solvent-accessible surface distance as the shortest path between two amino acids that traverses solvent-occupied space without penetrating the protein surface.

Scientific Applications:

• Structural Restraints for Modeling: Generates distance restraints to inform topology and three-dimensional modeling of proteins and protein complexes.
• Proteomics and Interaction Analysis: Aids interpretation of chemical cross-linking mass spectrometry data to study molecular interactions, conformational changes, and functional mechanisms.

Methodology:

Calculates SASD by finding the shortest solvent-accessible path on protein surfaces while accounting for protein surface topology and cross-linker non-linearity and flexibility.