TOPOLINK is a package to compute topological distances between
atoms on the surface of proteins and validate structural models using cross-linking
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
TopoLink is a package designed to compute topological distances and
evaluate structural models, structured with the experimental result in
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
TopoLink: Evaluation structural models using chemical crosslinking distance constraints.
Bioinformatics, 2019. [LINK]
Intra-protein predicted links
Inter-chain links of a complex