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

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Authors	VELECKÝ Jan BEREZNÝ Matej MUSIL Miloš DAMBORSKÝ Jiří BEDNÁŘ David MAZURENKO Stanislav
Year of publication	2024
Type	Article in Periodical
Magazine / Source	BIOINFORMATICS
MU Faculty or unit	Faculty of Science
Citation
web	https://academic.oup.com/bioinformatics/article/40/9/btae553/7755040?login=true
Doi	http://dx.doi.org/10.1093/bioinformatics/btae553
Keywords	PROTEIN STABILITY; SERVER; MUTATIONS; CHALLENGES
Attached files	2434258.pdf 2434258_published_version.pdf
Description	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.Availability and implementation BenchStab is an open-source Python package available at https://github.com/loschmidt/BenchStab with a detailed README and example usage at https://loschmidt.chemi.muni.cz/benchstab. The BenchStab dataset is available on Zenodo: https://zenodo.org/records/10637728
Related projects:	CETOCOEN Excellence e-Infrastruktura CZ Národní ústav pro neurologický výzkum ELIXIR-CZ: Czech National Infrastructure for Biological Data RECETOX research infrastructure