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

J 2016

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

BENDL, J., Jan ŠTOURAČ, Eva ŠEBESTOVÁ, Ondřej VÁVRA, Miloš MUSIL et. al.

Základní údaje

Originální název

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

Autoři

BENDL, J. (203 Česká republika), Jan ŠTOURAČ (203 Česká republika, domácí), Eva ŠEBESTOVÁ (203 Česká republika, domácí), Ondřej VÁVRA (203 Česká republika, domácí), Miloš MUSIL (203 Česká republika, domácí), Jan BREZOVSKÝ (203 Česká republika, domácí) a Jiří DAMBORSKÝ (203 Česká republika, garant, domácí)

Vydání

Nucleic Acids Research, Oxford University Press, 2016, 0305-1048

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10600 1.6 Biological sciences

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 10.162

Kód RIV

RIV/00216224:14310/16:00088547

Organizační jednotka

Přírodovědecká fakulta

DOI

http://dx.doi.org/10.1093/nar/gkw416

UT WoS

000379786800079

Klíčová slova anglicky

MULTIPLE SEQUENCE ALIGNMENTS; FUNCTIONALLY IMPORTANT RESIDUES; FOCUSED DIRECTED EVOLUTION; SATURATION MUTAGENESIS; CORRELATED MUTATIONS; ENZYME PROPERTIES; THERMOSTABILITY; IDENTIFICATION; CONSERVATION; BINDING

Štítky

AKR, rivok

Změněno: 6. 4. 2017 18:39, Ing. Andrea Mikešková

Anotace

V originále

HotSpot Wizard 2.0 is a web server for automated identification of hot spots and design of smart libraries for engineering proteins’ stability, catalytic activity, substrate specificity and enantioselectivity. The server integrates sequence, structural and evolutionary information obtained from 3 databases and 20 computational tools. Users are guided through the processes of selecting hot spots using four different protein engineering strategies and optimizing the resulting library’s size by narrowing down a set of substitutions at individual randomized positions. The only required input is a query protein structure. The results of the calculations are mapped onto the protein’s structure and visualized with a JSmol applet. HotSpot Wizard lists annotated residues suitable for mutagenesis and can automatically design appropriate codons for each implemented strategy. Overall, HotSpot Wizard provides comprehensive annotations of protein structures and assists protein engineers with the rational design of site-specific mutations and focused libraries. It is freely available at http://loschmidt.chemi.muni.cz/hotspotwizard.

Návaznosti

GA16-06096S, projekt VaV

Název: Objasnění významu dynamických tunelů pro enzymatickou katalýzu: simulace a fluorescenční experimenty

Investor: Grantová agentura ČR, Objasnění významu dynamických tunelů pro enzymatickou katalýzu: simulace a fluorescenční experimenty

LM2015047, projekt VaV

Název: Česká národní infrastruktura pro biologická data (Akronym: ELIXIR-CZ)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Česká národní infrastruktura pro biologická data

LM2015055, projekt VaV

Název: Centrum pro systémovou biologii (Akronym: C4SYS)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, The national infrastructure C4SYS - Centre for Systems Biology

LO1214, projekt VaV

Název: Centrum pro výzkum toxických látek v prostředí (Akronym: RECETOX)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Centrum pro výzkum toxických látek v prostředí

Citovat

BENDL, J., Jan ŠTOURAČ, Eva ŠEBESTOVÁ, Ondřej VÁVRA, Miloš MUSIL, Jan BREZOVSKÝ a Jiří DAMBORSKÝ. HotSpot Wizard 2.0: Automated Design of Site-Specific Mutations and Smart Libraries in Protein Engineering. Nucleic Acids Research. Oxford University Press, 2016, roč. 44, W1, s. "W479"-"W487", 9 s. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkw416.

@article{1367555,
   author = {Bendl, J. and Štourač, Jan and Šebestová, Eva and Vávra, Ondřej and Musil, Miloš and Brezovský, Jan and Damborský, Jiří},
   article_number = {W1},
   doi = {http://dx.doi.org/10.1093/nar/gkw416},
   keywords = {MULTIPLE SEQUENCE ALIGNMENTS; FUNCTIONALLY IMPORTANT RESIDUES; FOCUSED DIRECTED EVOLUTION; SATURATION MUTAGENESIS; CORRELATED MUTATIONS; ENZYME PROPERTIES; THERMOSTABILITY; IDENTIFICATION; CONSERVATION; BINDING},
   language = {eng},
   issn = {0305-1048},
   journal = {Nucleic Acids Research},
   title = {HotSpot Wizard 2.0: Automated Design of Site-Specific Mutations and Smart Libraries in Protein Engineering},
   url = {https://loschmidt.chemi.muni.cz/peg/wp-content/uploads/2016/05/Bendl_2016NAR.pdf},
   volume = {44},
   year = {2016}
}

TY  - JOUR
ID  - 1367555
AU  - Bendl, J. - Štourač, Jan - Šebestová, Eva - Vávra, Ondřej - Musil, Miloš - Brezovský, Jan - Damborský, Jiří
PY  - 2016
TI  - HotSpot Wizard 2.0: Automated Design of Site-Specific Mutations and Smart Libraries in Protein Engineering
JF  - Nucleic Acids Research
VL  - 44
IS  - W1
SP  - "W479"-"W487"
EP  - "W479"-"W487"
PB  - Oxford University Press
SN  - 03051048
KW  - MULTIPLE SEQUENCE ALIGNMENTS
KW  - FUNCTIONALLY IMPORTANT RESIDUES
KW  - FOCUSED DIRECTED EVOLUTION
KW  - SATURATION MUTAGENESIS
KW  - CORRELATED MUTATIONS
KW  - ENZYME PROPERTIES
KW  - THERMOSTABILITY
KW  - IDENTIFICATION
KW  - CONSERVATION
KW  - BINDING
UR  - https://loschmidt.chemi.muni.cz/peg/wp-content/uploads/2016/05/Bendl_2016NAR.pdf
L2  - https://loschmidt.chemi.muni.cz/peg/wp-content/uploads/2016/05/Bendl_2016NAR.pdf
N2  - HotSpot Wizard 2.0 is a web server for automated identification of hot spots and design of smart libraries for engineering proteins’ stability, catalytic activity, substrate specificity and enantioselectivity. The server integrates sequence, structural and evolutionary information obtained from 3 databases and 20 computational tools. Users are guided through the processes of selecting hot spots using four different protein engineering strategies and optimizing the resulting library’s size by narrowing down a set of substitutions at individual randomized positions. The only required input is a query protein structure. The results of the calculations are mapped onto the protein’s structure and visualized with a JSmol applet. HotSpot Wizard lists annotated residues suitable for mutagenesis and can automatically design appropriate codons for each implemented strategy. Overall, HotSpot Wizard provides comprehensive annotations of protein structures and assists protein engineers with the rational design of site-specific mutations and focused libraries. It is freely available at http://loschmidt.chemi.muni.cz/hotspotwizard.
ER  -

BENDL, J., Jan ŠTOURAČ, Eva ŠEBESTOVÁ, Ondřej VÁVRA, Miloš MUSIL, Jan BREZOVSKÝ a Jiří DAMBORSKÝ. HotSpot Wizard 2.0: Automated Design of Site-Specific Mutations and Smart Libraries in Protein Engineering. \textit{Nucleic Acids Research}. Oxford University Press, 2016, roč.~44, W1, s.~''W479''-''W487'', 9 s. ISSN~0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkw416.

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