Related Experiment Video
Updated: Jan 30, 2026

BS3 Chemical Crosslinking Assay: Evaluating the Effect of Chronic Stress on Cell Surface GABAA Receptor Presentation in the Rodent Brain
Published on: May 26, 2023
TopoLink: evaluation of structural models using chemical crosslinking distance constraints
Allan J R Ferrari1, Milan A Clasen2, Louise Kurt2
1Institute of Chemistry, University of Campinas, Campinas, SP, Brazil.
Summary:
A software was developed to evaluate structural models using chemical crosslinking experiments. The user provides the types of linkers used and their reactivity, and the observed crosslinks and dead-ends. The software computes the minimum length of a physically inspired linker that connects the reactive atoms of interest, and reports the consistency of each distance with the experimental observation. Statistics on model consistency with the links are provided. Tools to evaluate the correlation of crosslinks in ensembles of models were developed. TopoLink was used to evaluate the potential crosslinks of all structures of the CATH database. The number of crosslinks expected as a function of protein size and linker length can be used as guide for experimental design.
Availability And Implementation:
TopoLink is available as free software at http://m3g.iqm.unicamp.br/topolink, and distributed as source code with a user-friendly graphical interface for Windows. A web server is also provided.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
More Related Videos
05:18Quaternary Structure Modeling Through Chemical Cross-Linking Mass Spectrometry: Extending TX-MS Jupyter Reports
Published on: October 20, 2021
14:02Optimizing the Genetic Incorporation of Chemical Probes into GPCRs for Photo-crosslinking Mapping and Bioorthogonal Chemistry in Live Mammalian Cells
Published on: April 9, 2018
Related Concept Videos
Distance Problem
Short-distance Transport of Resources
Chemical Formulas
Constraints and Statical Determinacy
The Distance Formula
Distance Corrections