Detail publikace

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.

Originální název

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

Typ

článek v časopise ve Scopus, Jsc

Jazyk

angličtina

Originální abstrakt

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.

Klíčová slova

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

Autoři

MUSIL, M.; JEŽÍK, A.; HORÁČKOVÁ, J.; BORKO, S.; KABOUREK, P.; DAMBORSKÝ, J.; BEDNÁŘ, D.

Vydáno

2. 11. 2023

ISSN

1467-5463

Periodikum

BRIEFINGS IN BIOINFORMATICS

Ročník

25

Číslo

1

Stát

Spojené království Velké Británie a Severního Irska

Strany od

1

Strany do

10

Strany počet

17

URL

https://www.fit.vut.cz/research/publication/13097/

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/"
}

Dokumenty

FireProt2.pdf
Supplementary_table_S2.xlsx
Supplementary_table_S1.xlsx
Supplementary_table_S3.xlsx