TopoLink: Evaluation of structural models using chemical crosslinking distance constraints

Allan J.R. Ferrari; Milan A. Clasen; Louise Kurt; Paulo C. Carvalho; Fabio C. Gozzo; Leandro Martínez

doi:10.1093/bioinformatics/btz014

TopoLink: Evaluation of structural models using chemical crosslinking distance constraints

Allan J.R. Ferrari, Milan A. Clasen, Louise Kurt, Paulo C. Carvalho, Fabio C. Gozzo, Leandro Martínez^*

^*Corresponding author for this work

Pharmacology

Research output: Contribution to journal › Article › peer-review

17 Scopus citations

Abstract

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.

Original language	English (US)
Pages (from-to)	3169-3170
Number of pages	2
Journal	Bioinformatics
Volume	35
Issue number	17
DOIs	https://doi.org/10.1093/bioinformatics/btz014
State	Published - Sep 1 2019

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btz014

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title = "TopoLink: Evaluation of structural models using chemical crosslinking distance constraints",

abstract = "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.",

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AU - Clasen, Milan A.

AU - Kurt, Louise

AU - Carvalho, Paulo C.

AU - Gozzo, Fabio C.

AU - Martínez, Leandro

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TopoLink: Evaluation of structural models using chemical crosslinking distance constraints

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