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

Bioinformatics. 2019 Sep 1;35(17):3169-3170. doi: 10.1093/bioinformatics/btz014.

Authors

Allan J R Ferrari¹, Milan A Clasen², Louise Kurt², Paulo C Carvalho², Fabio C Gozzo¹, Leandro Martínez^{1

3}

Affiliations

¹ Institute of Chemistry, University of Campinas, Campinas, SP, Brazil.
² Carlos Chagas Institute, Fiocruz, Brazil.
³ Center for Computing in Engineering & Sciences, University of Campinas, Campinas, SP, Brazil.

PMID: 30629147
DOI: 10.1093/bioinformatics/btz014

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computers
Proteins
Software*

Substances

Proteins