NRGXL

NRGXL performs quantitative structural interpretation of protein crosslinks using chemical crosslinking and mass spectrometry data by integrating crosslinker and side-chain conformational sampling with physico-chemical energy calculations.

Key Features:

• Flexibility Modeling: Incorporates flexibility of both the crosslinker and linked side-chains by explicitly sampling numerous conformations for more realistic structural restraints.
• Physico-Chemical Interactions: Accounts for physico-chemical interactions between the crosslinker and the protein and includes associated energy calculations.
• Protein Dynamics Consideration: Handles overall protein dynamics to support interpretation of crosslinks in complex biological systems.
• Classifier Performance: Employs a classifier based on the detailed physical modeling that outperforms classifiers using Euclidean distance or solvent-accessible distance metrics for validating 3D models from crosslinking data.

Scientific Applications:

• Structural model validation and refinement: Validates and refines 3D models of proteins and large assemblies derived from crosslinking mass spectrometry.
• Integration with molecular modeling: Interprets chemical crosslinking and mass spectrometry data within molecular modeling frameworks for structural analysis.
• Analysis of protein dynamics and interactions: Enables analysis of protein dynamics, function, and interactions within larger complexes.

Methodology:

Constructs a physical model that explicitly samples multiple conformations of the crosslinker and linked side-chains, integrates energy calculations for physico-chemical interactions, and applies a classifier based on this modeling to validate 3D models.