Journal
NUCLEIC ACIDS RESEARCH
Volume 46, Issue W1, Pages W356-W362Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gky417
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Funding
- Ministry of Education, Youth and Sports of the Czech Republic from the National Programme of Sustainability II [LQ1602, LQ1605, LO1214]
- European Regional Development Fund [LM2015051, LM2015047, LM2015055]
- Grant Agency of the Czech Republic [16-06096S]
- European Union [720776, 722610]
- Brno University Technology [FIT-S-17-3994]
- Czech Ministry of Education
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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.
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