XLM-Tools

XLM-Tools integrates crosslink and monolink data from Chemical Crosslinking Mass Spectrometry (CCMS) to score and evaluate protein structural models using Monolink Depth Score (MoDS), MNXL crosslink scoring, and an integrated XLMO score.

Key Features:

• Monolink Depth Score (MoDS): Evaluates protein structure models based on the depth of monolinked residues measured as the distance from the nearest bulk water.
• Crosslink Scoring with MNXL: Incorporates MNXL (Mass Spectrometry-based Network Crosslinking) to assess protein models using crosslink data and distance constraints.
• Integrated XLMO Score: Combines MoDS and MNXL when both monolink and crosslink data are available to produce an integrated score that improves model evaluation.

Scientific Applications:

• Integrative structural biology: Refines and validates protein structural models by integrating CCMS-derived crosslink and monolink information, including underexploited monolink data.

Methodology:

Development and validation used simulated and reprocessed experimental datasets from the Proteomic Identification Database (PRIDE), and comparative analyses demonstrated MoDS scoring of monolink data and improved model evaluation when MoDS is combined with MNXL into the XLMO score.