Jwalk and MNXL web server: model validation using restraints from crosslinking mass spectrometry

Area of Science:

• Structural biology
• Computational biology
• Biochemistry

Background:

• Crosslinking Mass Spectrometry (CMS) provides distance restraints crucial for protein structure modeling.
• Previous methods, Jwalk and MNXL, were developed to enhance the utilization of CMS restraints for improved modeling.
• Accurate protein modeling relies on high-quality experimental data and robust validation techniques.

Purpose of the Study:

• To present user-friendly webservers for Jwalk and MNXL, facilitating the validation of protein models.
• To streamline the process of assessing the quality of structural models generated using CMS data.
• To enable researchers to filter and select the most biologically relevant protein models.

Main Methods:

• Development and deployment of Jwalk and MNXL as accessible webservers.
• Utilizing Jwalk to estimate solvent accessible distances between crosslinked residues.
• Employing MNXL for the quality assessment of protein models based on crosslinking restraints.

Main Results:

• The Jwalk and MNXL webservers are now available, simplifying the validation of monomeric protein models.
• Demonstrated the utility of the MNXL server in filtering protein models of varying quality.
• Successfully identified and selected the most native-like models from a set of candidates.

Conclusions:

• The Jwalk and MNXL webservers offer valuable tools for the structural biology community.
• These webservers enhance the reliability and accuracy of protein structure modeling using CMS data.
• Freely available resources promote reproducible research and advance protein structure determination.