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Method Article
Leandro Martinez
Martinez's Molecular Modeling Lab, Institute of Chemistry - University of Campinas
Corresponding Author
License:
This work is licensed under a CC BY-NC 3.0 License. Read Full License
TOPOLINK is a package to compute topological distances between atoms on the surface of proteins and validate structural models from cross-linking experimental data.
The package is available at:
"http://leandro.iqm.unicamp.br/topolink":http://leandro.iqm.unicamp.br/topolink
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 consistent with that experimental results.
For doing so, TopoLink computes all possible cross-links of the structure and their consistency with experimental observations. It also provides means for the visualization of the topological distances on the protein structure.
Keywords
chemical crosslinking, mass spectrometry, protein modeling, rosetta
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Posted 25 Mar, 2017
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An open repository of community-contributed protocols sponsored by Nature Research.
Learn more about Protocol Exchange
Method Article
Leandro Martinez
Martinez's Molecular Modeling Lab, Institute of Chemistry - University of Campinas
Corresponding Author
Version History
CURRENT STATUS: Posted
Version 1
Posted 25 Mar, 2017
Community comments: 1
Metrics
Comments: 0
HTML Views: ...
License:
This work is licensed under a CC BY-NC 3.0 License. Read Full License
TOPOLINK is a package to compute topological distances between atoms on the surface of proteins and validate structural models from cross-linking experimental data.
The package is available at:
"http://leandro.iqm.unicamp.br/topolink":http://leandro.iqm.unicamp.br/topolink
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 consistent with that experimental results.
For doing so, TopoLink computes all possible cross-links of the structure and their consistency with experimental observations. It also provides means for the visualization of the topological distances on the protein structure.
Figure 1
none
Loading...