Publication Details

HotSpot Wizard 2.0: Automated Design of Site-specific Mutations and Smart Libraries in Protein Engineering

BENDL, J.; ŠTOURAČ, J.; ŠEBESTOVÁ, E.; VÁVRA, O.; MUSIL, M.; BREZOVSKÝ, J.; DAMBORSKÝ, J. HotSpot Wizard 2.0: Automated Design of Site-specific Mutations and Smart Libraries in Protein Engineering. Nucleic Acids Research, 2016, vol. 44, no. 1, p. 479-487. ISSN: 1362-4962.
Czech title
HotSpot Wizard 2.0: Automatický návrh místně-specifických mutací a chytrých knihoven pro proteinové inženýrství
Type
journal article
Language
English
Authors
Bendl Jaroslav, Ing., Ph.D.
Štourač Jan (FIT)
Chovancová Eva, Mgr., Ph.D. (FIT)
Vávra Ondřej
Musil Miloš, Ing., Ph.D. (DIFS)
Brezovský Jan (FIT)
Damborský Jiří, prof. Mgr., Dr. (UMEL)
URL
Keywords

protein engineering, smart library design, computational mutagenesis, hotspot prediction, semi-rational enzyme design

Abstract

HotSpot Wizard 2.0 is a web server for an automatic identification of hot spots and design of mutations for engineering of enzyme activity, substrate specificity, and enantioselectivity or protein stability. The server integrates sequence, structural, and evolutionary information obtained from three databases and nineteen computational tools to guide the users through the process of hot spot selection by four protein engineering strategies as well as the optimization of library size by narrowing down a set of substitutions at individual randomized positions. The protein structure represents the only obligatory input for the calculation. The results of calculations are mapped on the protein structure and visualized in JSMol applet. For each implemented strategy, HotSpot Wizard lists annotated residues suitable for mutagenesis and enables to design appropriate codons. Altogether, HotSpot Wizard provides a comprehensive annotation of protein structures and assists protein engineers with the design of mutations in site-directed mutagenesis and focused directed evolution experiments. HotSpot Wizard is freely available at http://loschmidt.chemi.muni.cz/hotspotwizard2.

Published
2016
Pages
479–487
Journal
Nucleic Acids Research, vol. 44, no. 1, ISSN 1362-4962
DOI
10.1093/nar/gkp410
UT WoS
000379786800079
EID Scopus
2-s2.0-85018064697
BibTeX 
@article{BUT133492,
  author="Jaroslav {Bendl} and Jan {Štourač} and Eva {Chovancová} and Ondřej {Vávra} and Miloš {Musil} and Jan {Brezovský} and Jiří {Damborský}",
  title="HotSpot Wizard 2.0: Automated Design of Site-specific Mutations and Smart Libraries in Protein Engineering",
  journal="Nucleic Acids Research",
  year="2016",
  volume="44",
  number="1",
  pages="479--487",
  doi="10.1093/nar/gkp410",
  issn="1362-4962",
  url="http://nar.oxfordjournals.org/content/early/2016/05/12/nar.gkw416.full"
}
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