Publication Details

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

VELECKÝ, J.; BEREZNÝ, M.; MUSIL, M.; MAZURENKO, S.; BEDNÁŘ, D.; DAMBORSKÝ, J. BenchStab: A tool for automated querying of web-based stability predictors. BIOINFORMATICS, 2024, vol. 2024, no. 9, p. 1-8. ISSN: 1367-4803.

Czech title

BenchStab: nástroj pro automatické vyhodnocení webových prediktorů stability

Type

journal article

Language

English

Authors

Velecký Jan, Ing.
Berezný Matej, Ing.
Musil Miloš, Ing., Ph.D. (DIFS)
Mazurenko Stanislav, Ph.D.
Bednář David (FIT)
Damborský Jiří, prof. Mgr., Dr. (UMEL)

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

DOI

10.1093/bioinformatics/btae553

BibTeX

@article{BUT189729,
  author="Jan {Velecký} and Matej {Berezný} and Miloš {Musil} and Stanislav {Mazurenko} and David {Bednář} and Jiří {Damborský}",
  title="BenchStab: A tool for automated querying of web-based stability predictors",
  journal="BIOINFORMATICS",
  year="2024",
  volume="2024",
  number="9",
  pages="1--8",
  doi="10.1093/bioinformatics/btae553",
  issn="1367-4803",
  url="https://academic.oup.com/bioinformatics/article/40/9/btae553/7755040"
}