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.

Basic information

Original name

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

Authors

BENDL, J. (203 Czech Republic), Jan ŠTOURAČ (203 Czech Republic, belonging to the institution), Eva ŠEBESTOVÁ (203 Czech Republic, belonging to the institution), Ondřej VÁVRA (203 Czech Republic, belonging to the institution), Miloš MUSIL (203 Czech Republic, belonging to the institution), Jan BREZOVSKÝ (203 Czech Republic, belonging to the institution) and Jiří DAMBORSKÝ (203 Czech Republic, guarantor, belonging to the institution)

Edition

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

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 10.162

RIV identification code

RIV/00216224:14310/16:00088547

Organization unit

Faculty of Science

DOI

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

UT WoS

000379786800079

Keywords in English

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

Abstract

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.

Links

GA16-06096S, research and development project

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

Investor: Czech Science Foundation

LM2015047, research and development project

Name: Česká národní infrastruktura pro biologická data (Acronym: ELIXIR-CZ)

Investor: Ministry of Education, Youth and Sports of the CR, Czech National Infrastructure for Biological Data

LM2015055, research and development project

Name: Centrum pro systémovou biologii (Acronym: C4SYS)

Investor: Ministry of Education, Youth and Sports of the CR

LO1214, research and development project

Name: Centrum pro výzkum toxických látek v prostředí (Acronym: RECETOX)

Investor: Ministry of Education, Youth and Sports of the CR

Citovat

BENDL, J., Jan ŠTOURAČ, Eva ŠEBESTOVÁ, Ondřej VÁVRA, Miloš MUSIL, Jan BREZOVSKÝ and 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, vol. 44, W1, p. "W479"-"W487", 9 pp. ISSN 0305-1048. Available from: 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 and 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, vol.~44, W1, p.~''W479''-''W487'', 9 pp. ISSN~0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkw416.

Detailed Information on Publication Record