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DE-STRESS: a user-friendly web application for the evaluation of protein designs

De novo protein design is a rapidly growing field, and there are now many interesting and useful examples of designed proteins in the literature. However, most designs could be classed as failures when characterised in the lab, usually as a result of low expression, misfolding, aggregation or lack o...

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Detalles Bibliográficos
Autores principales: Stam, Michael J, Wood, Christopher W
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8672653/
https://www.ncbi.nlm.nih.gov/pubmed/34908138
http://dx.doi.org/10.1093/protein/gzab029
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author Stam, Michael J
Wood, Christopher W
author_facet Stam, Michael J
Wood, Christopher W
author_sort Stam, Michael J
collection PubMed
description De novo protein design is a rapidly growing field, and there are now many interesting and useful examples of designed proteins in the literature. However, most designs could be classed as failures when characterised in the lab, usually as a result of low expression, misfolding, aggregation or lack of function. This high attrition rate makes protein design unreliable and costly. It is possible that some of these failures could be caught earlier in the design process if it were quick and easy to generate information and a set of high-quality metrics regarding designs, which could be used to make reproducible and data-driven decisions about which designs to characterise experimentally. We present DE-STRESS (DEsigned STRucture Evaluation ServiceS), a web application for evaluating structural models of designed and engineered proteins. DE-STRESS has been designed to be simple, intuitive to use and responsive. It provides a wealth of information regarding designs, as well as tools to help contextualise the results and formally describe the properties that a design requires to be fit for purpose.
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spelling pubmed-86726532021-12-16 DE-STRESS: a user-friendly web application for the evaluation of protein designs Stam, Michael J Wood, Christopher W Protein Eng Des Sel Short Communication De novo protein design is a rapidly growing field, and there are now many interesting and useful examples of designed proteins in the literature. However, most designs could be classed as failures when characterised in the lab, usually as a result of low expression, misfolding, aggregation or lack of function. This high attrition rate makes protein design unreliable and costly. It is possible that some of these failures could be caught earlier in the design process if it were quick and easy to generate information and a set of high-quality metrics regarding designs, which could be used to make reproducible and data-driven decisions about which designs to characterise experimentally. We present DE-STRESS (DEsigned STRucture Evaluation ServiceS), a web application for evaluating structural models of designed and engineered proteins. DE-STRESS has been designed to be simple, intuitive to use and responsive. It provides a wealth of information regarding designs, as well as tools to help contextualise the results and formally describe the properties that a design requires to be fit for purpose. Oxford University Press 2021-12-15 /pmc/articles/PMC8672653/ /pubmed/34908138 http://dx.doi.org/10.1093/protein/gzab029 Text en © The Author(s) 2021. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Short Communication
Stam, Michael J
Wood, Christopher W
DE-STRESS: a user-friendly web application for the evaluation of protein designs
title DE-STRESS: a user-friendly web application for the evaluation of protein designs
title_full DE-STRESS: a user-friendly web application for the evaluation of protein designs
title_fullStr DE-STRESS: a user-friendly web application for the evaluation of protein designs
title_full_unstemmed DE-STRESS: a user-friendly web application for the evaluation of protein designs
title_short DE-STRESS: a user-friendly web application for the evaluation of protein designs
title_sort de-stress: a user-friendly web application for the evaluation of protein designs
topic Short Communication
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8672653/
https://www.ncbi.nlm.nih.gov/pubmed/34908138
http://dx.doi.org/10.1093/protein/gzab029
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