Working Paper Review Version 2 This version is not peer-reviewed

Web-Based Tools for Computational Enzyme Design

Version 1 : Received: 2 December 2020 / Approved: 3 December 2020 / Online: 3 December 2020 (14:33:54 CET)
Version 2 : Received: 27 January 2021 / Approved: 28 January 2021 / Online: 28 January 2021 (07:51:45 CET)

How to cite: Marques, S.M.; Planas-Iglesias, J.; Damborsky, J. Web-Based Tools for Computational Enzyme Design. Preprints 2020, 2020120089 Marques, S.M.; Planas-Iglesias, J.; Damborsky, J. Web-Based Tools for Computational Enzyme Design. Preprints 2020, 2020120089

Abstract

Enzymes are in high demand for very diverse biotechnological applications. However, natural biocatalysts often need to be engineered for fine-tuning their properties towards the end applications, such as the activity, selectivity, stability to temperature or co-solvents, and solubility. Computational methods are increasingly used in this task, providing predictions that narrow down the space of possible mutations significantly and can enormously reduce the experimental burden. Many computational tools are available as web-based platforms, making them accessible to non-expert users. These platforms are typically user-friendly, contain walk-throughs, and do not require deep expertise and installations. Here we describe some of the most recent outstanding web-tools for enzyme engineering and formulate future perspectives in this field.

Subject Areas

web server; rational design; functionalizing enzymes; enzyme discovery; user-friendly tools

Comments (1)

Comment 1
Received: 28 January 2021
Commenter: Sérgio M. Marques
Commenter's Conflict of Interests: Author
Comment: This is the second version after addressing the revewers comments.
The main changes are:
1) We added to Table 1 a description for every tool of how they were validated, in many cases reporting experimental data to support their robustness. This can add relevant information for the interested user to them choosing which tool to use in their particular projects.
2) The addition of LoopGrafter, a new webserver recently launched by our group devoted to the redesign of protein loops, and submitted for publication.
3) Monor improvement of the conclusions.
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