Result 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. 40, no. 9, p. 1-8. ISSN: 1367-4803.
Type
journal article
Language
English
Authors
Velecký Jan, Ing.
Berezný Matej, Ing.
Musil Miloš, Ing., Ph.D., DIFS (FIT)
Damborský Jiří, prof. Mgr., Dr., UMEL (FEEC)
Bednář David, FIT (FIT)
Mazurenko Stanislav, Ph.D.
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.

Keywords

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

URL
Published
2024
Pages
1–8
Journal
BIOINFORMATICS, vol. 40, no. 9, ISSN 1367-4803
Publisher
Oxford University Press
DOI
10.1093/bioinformatics/btae553
UT WoS
001320121300001
EID Scopus
2-s2.0-85205274889
BibTeX 
@article{BUT189729,
  author="Jan {Velecký} and Matej {Berezný} and Miloš {Musil} and Jiří {Damborský} and David {Bednář} and Stanislav {Mazurenko}",
  title="BenchStab: A tool for automated querying of web-based stability predictors",
  journal="BIOINFORMATICS",
  year="2024",
  volume="40",
  number="9",
  pages="1--8",
  doi="10.1093/bioinformatics/btae553",
  issn="1367-4803",
  url="https://academic.oup.com/bioinformatics/article/40/9/btae553/7755040"
}
Files
Projects
Chytré informační technologie pro odolnou společnost, BUT, Vnitřní projekty VUT, FIT-S-23-8209, start: 2023-03-01, end: 2026-02-28, running
Departments
Department of Information Systems (DIFS)
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