Publication Details

FireProt 2.0: Web-based Platform for the Fully-Automated Design of Thermostable Proteins

MUSIL, M.; JEŽÍK, A.; HORÁČKOVÁ, J.; BORKO, S.; KABOUREK, P.; DAMBORSKÝ, J.; BEDNÁŘ, D. FireProt 2.0: Web-based Platform for the Fully-Automated Design of Thermostable Proteins. BRIEFINGS IN BIOINFORMATICS, 2023, vol. 25, no. 1, p. 1-10. ISSN: 1467-5463.
Czech title
FireProt 2.0: Webová platforma pro plně automatizovaný návrh stabilních proteinů
Type
journal article
Language
English
Authors
Musil Miloš, Ing., Ph.D. (DIFS)
Ježík Andrej, Bc.
Horáčková Jana, Mgr.
Borko Simeon, Ing.
Kabourek Petr
Damborský Jiří, prof. Mgr., Dr. (UMEL)
Bednář David
Keywords

ancestral, back-to-consensus, B-factor,
epistasis, evolution, force-field, multiple-point mutant, protein engineering, saturation
mutagenesis, thermostability

Abstract

Thermostable proteins find their use
in numerous biomedical and biotechnological applications. However, the
computational design of stable proteins often results in single-point mutations
with a limited effect on protein stability. However, the construction of stable multiple-point
mutants can prove difficult due to the possibility of antagonistic effects
between individual mutations. FireProt protocol enables the automated
computational design of highly stable multiple-point mutants. FireProt 2.0
builds on top of the previously published FireProt web, retaining the original
functionality and expanding it with several new stabilization strategies. FireProt
2.0 integrates the AlphaFold database and the homology modelling for structure
prediction, enabling calculations starting from a sequence. Multiple-point
designs are constructed using the Bron-Kerbosch algorithm minimizing the
antagonistic effect between the individual mutations. Users can newly limit the
FireProt calculation to a set of user-defined mutations, run a saturation
mutagenesis of the whole protein, or select rigidifying mutations based on B-factors.
Evolution-based back-to-consensus strategy is complemented by ancestral
sequence reconstruction. FireProt 2.0 is significantly faster and a reworked graphical
user interface broadens the tool's availability even to users with older
hardware. FireProt 2.0 is freely available at http://loschmidt.chemi.muni.cz/fireprotweb.

Published
2023
Pages
1–10
Journal
BRIEFINGS IN BIOINFORMATICS, vol. 25, no. 1, ISSN 1467-5463
DOI
10.1093/bib/bbad425
UT WoS
001173375300007
EID Scopus
2-s2.0-85179485662
BibTeX 
@article{BUT185670,
  author="Miloš {Musil} and Andrej {Ježík} and Jana {Horáčková} and Simeon {Borko} and Petr {Kabourek} and Jiří {Damborský} and David {Bednář}",
  title="FireProt 2.0: Web-based Platform for the Fully-Automated Design of Thermostable Proteins",
  journal="BRIEFINGS IN BIOINFORMATICS",
  year="2023",
  volume="25",
  number="1",
  pages="1--10",
  doi="10.1093/bib/bbad425",
  issn="1467-5463",
  url="https://www.fit.vut.cz/research/publication/13097/"
}
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