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Lookup NU author(s): Christian Atallah Atallah, Dr Katherine JamesORCiD, Zhen Ou, Dr James Skelton, David Markham, Matt Burridge, Professor Anil Wipat
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© 2023. Enzymes are being increasingly exploited for their potential as industrial biocatalysts. Establishing a portfolio of useful biocatalysts from large and diverse protein family is challenging and a systematic method for candidate selection promises to aid in this task. Moreover, accurate enzyme functional annotation can only be confidently guaranteed through experimental characterisation in the laboratory. The selection of catalytically diverse enzyme panels for experimental characterisation is also an important step for shedding light on the currently unannotated proteins in enzyme families. Current selection methods often lack efficiency and scalability, and are usually non-systematic. We present a novel algorithm for the automatic selection of subsets from enzyme families. A tabu search algorithm solving the maximum diversity problem for sequence identity was designed and implemented, and applied to three diverse enzyme families. We show that this approach automatically selects panels of enzymes that contain high richness and relative abundance of the known catalytic functions, and outperforms other methods such as k-medoids.
Author(s): Atallah C, James K, Ou Z, Skelton J, Markham D, Burridge MS, Finnigan J, Charnock S, Wipat A
Publication type: Article
Publication status: Published
Journal: BioSystems
Year: 2024
Volume: 236
Print publication date: 01/02/2024
Online publication date: 29/12/2023
Acceptance date: 15/12/2023
ISSN (print): 0303-2647
ISSN (electronic): 1872-8324
Publisher: Elsevier Ireland Ltd
URL: https://doi.org/10.1016/j.biosystems.2023.105105
DOI: 10.1016/j.biosystems.2023.105105
PubMed id: 38160995
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