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A method for the systematic selection of enzyme panel candidates by solving the maximum diversity problem

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.

Publication metadata

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


DOI: 10.1016/j.biosystems.2023.105105

PubMed id: 38160995


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