Publication Details

BenchStab: A tool for automated querying of web-based stability predictors

VELECKÝ Jan, BEREZNÝ Matej, MUSIL Miloš, MAZURENKO Stanislav, BEDNÁŘ David and DAMBORSKÝ Jiří. BenchStab: A tool for automated querying of web-based stability predictors. Bioinformatics, vol. 2024, no. 9, pp. 1-8. ISSN 1367-4803.
Czech title
BenchStab: nástroj pro automatické vyhodnocení webových prediktorů stability
Type
journal article
Language
english
Authors
Velecký Jan, Ing. (FIT BUT)
Berezný Matej, Ing. (FIT BUT)
Musil Miloš, Ing., Ph.D. (DIFS FIT BUT)
Mazurenko Stanislav, Ph.D. (LL)
Bednář David, Mgr. (LL)
Damborský Jiří, prof. Mgr., Dr. (LL)
URL
Keywords

prediction of stability, protein stability, web-tools, benchmarking

Abstract

Protein design requires information about how mutations affect protein stability. Many web-based predictors are available for this purpose, yet comparing them or using them en masse is difficult. Here, we present BenchStab, a console tool/Python package for easy and quick execution of 19 predictors and result collection on a list of mutants. Moreover, the tool is easily extensible with additional predictors. We created an independent dataset derived from the FireProtDB and evaluated 24 different prediction methods.

Published
2024
Pages
1-8
Journal
Bioinformatics, vol. 2024, no. 9, ISSN 1367-4803
Publisher
Oxford University Press
DOI
10.1093/bioinformatics/btae553
BibTeX 
@ARTICLE{FITPUB13263,
   author = "Jan Veleck\'{y} and Matej Berezn\'{y} and Milo\v{s} Musil and Stanislav Mazurenko and David Bedn\'{a}\v{r} and Ji\v{r}\'{i} Damborsk\'{y}",
   title = "BenchStab: A tool for automated querying of web-based stability predictors",
   pages = "1--8",
   journal = "Bioinformatics",
   volume = 2024,
   number = 9,
   year = 2024,
   ISSN = "1367-4803",
   doi = "10.1093/bioinformatics/btae553",
   language = "english",
   url = "https://www.fit.vut.cz/research/publication/13263"
}
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