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

Abstract

Motivation Crosslinking Mass Spectrometry generates restraints that can be used to model proteins and protein complexes. Previously, we have developed two methods, to help users achieve better modelling performance from their crosslinking restraints: Jwalk, to estimate solvent accessible distances between crosslinked residues and MNXL, to assess the quality of the models based on these distances. Results Here, we present the Jwalk and MNXL webservers, which streamline the process of validating monomeric protein models using restraints from crosslinks. We demonstrate this by using the MNXL server to filter models made of varying quality, selecting the most native-like. Availability and implementation The webserver and source code are freely available from jwalk.ismb.lon.ac.uk and mnxl.ismb.lon.ac.uk. Supplementary informationSupplementary dataare available at Bioinformatics online.