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
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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