| SUMBALOVÁ, Lenka, Jan ŠTOURAČ, Tomáš MARTÍNEK, David BEDNÁŘ and Jiří DAMBORSKÝ. HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information. Nucleic Acids Research. Oxford: Oxford University Press, 2018, vol. 46, W1, p. "W356"-"W362", 7 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gky417. |
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@article{1503351,
author = {Sumbalová, Lenka and Štourač, Jan and Martínek, Tomáš and Bednář, David and Damborský, Jiří},
article_location = {Oxford},
article_number = {W1},
doi = {http://dx.doi.org/10.1093/nar/gky417},
keywords = {PROTEIN-STRUCTURE PREDICTION; DIRECTED EVOLUTION; HALOALKANE DEHALOGENASE},
language = {eng},
issn = {0305-1048},
journal = {Nucleic Acids Research},
title = {HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information},
url = {https://loschmidt.chemi.muni.cz/peg/category/publications/#2018},
volume = {46},
year = {2018}
}
TY - JOUR
ID - 1503351
AU - Sumbalová, Lenka - Štourač, Jan - Martínek, Tomáš - Bednář, David - Damborský, Jiří
PY - 2018
TI - HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information
JF - Nucleic Acids Research
VL - 46
IS - W1
SP - "W356"-"W362"
EP - "W356"-"W362"
PB - Oxford University Press
SN - 03051048
KW - PROTEIN-STRUCTURE PREDICTION
KW - DIRECTED EVOLUTION
KW - HALOALKANE DEHALOGENASE
UR - https://loschmidt.chemi.muni.cz/peg/category/publications/#2018
N2 - HotSpot Wizard is a web server used for the automated identification of hotspots in semi-rational protein design to give improved protein stability, catalytic activity, substrate specificity and enantioselectivity. Since there are three orders of magnitude fewer protein structures than sequences in bioinformatic databases, the major limitation to the usability of previous versions was the requirement for the protein structure to be a compulsory input for the calculation. HotSpot Wizard 3.0 now accepts the protein sequence as input data. The protein structure for the query sequence is obtained either from eight repositories of homology models or is modeled using Modeller and I-Tasser. The quality of the models is then evaluated using three quality assessment tools-WHAT_CHECK, PROCHECK and MolProbity. During follow-up analyses, the system automatically warns the users whenever they attempt to redesign poorly predicted parts of their homology models. The second main limitation of HotSpot Wizard's predictions is that it identifies suitable positions for mutagenesis, but does not provide any reliable advice on particular substitutions. A new module for the estimation of thermodynamic stabilities using the Rosetta and FoldX suites has been introduced which prevents destabilizing mutations among pre-selected variants entering experimental testing.
ER -
SUMBALOVÁ, Lenka, Jan ŠTOURAČ, Tomáš MARTÍNEK, David BEDNÁŘ and Jiří DAMBORSKÝ. HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information. \textit{Nucleic Acids Research}. Oxford: Oxford University Press, 2018, vol.~46, W1, p.~''W356''-''W362'', 7 pp. ISSN~0305-1048. Available from: https://dx.doi.org/10.1093/nar/gky417.
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