TOPOLINK

A package to evaluate structural models using chemical crosslinking distance constraints.

Institute of Chemistry
University of Campinas

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TOPOLINK is a package to compute topological distances between atoms on the surface of proteins and validate structural models using cross-linking experimental data.

Chemical cross-linking mass spectrometry is powerful experimental method for the evaluation of interatomic distances in biomolecular structures. These experiments provided upper bounds for the distances between residues, by the identification of pairs of atoms in the surface of protein which are within the linker reach.

The evaluation of structural models using chemical cross-linking depends on the determination of the topological, or surface-accessible, distances of the reactive residues in the model, and its comparison with experimental observations.

TopoLink is a package designed to compute topological distances and evaluate structural models, structured with the experimental result in mind.

The user provides a description of the experiments performed, the types of cross-links that can be formed in each experiment, and an account of the experimental result, and TopoLink determines how consistent a structural model is with the experimental results.

This consistency is evaluated by computing all possible cross-links of the structure and their correlation with experimental observations.

Supporting structure files are provided for the visualization of the topological distances on the protein structure, as exemplified in the figures.
A. J. R. Ferrari, M. A. Clasen, L. Kurt, P. C. Carvalho, F. C. Gozzo, L Martínez
TopoLink: Evaluation structural models using chemical crosslinking distance constraints.
Bioinformatics, 2019. [LINK]

Intra-protein predicted links

Inter-chain links of a complex