SelenzymeRF: updated enzyme suggestion software for unbalanced biochemical reactions.
Enzyme selection
RXNMapper
Reacting site
Reaction similarity
Retrobiosynthesis
Unbalanced reactions
Journal
Computational and structural biotechnology journal
ISSN: 2001-0370
Titre abrégé: Comput Struct Biotechnol J
Pays: Netherlands
ID NLM: 101585369
Informations de publication
Date de publication:
2023
2023
Historique:
medline:
11
12
2023
pubmed:
11
12
2023
entrez:
11
12
2023
Statut:
epublish
Résumé
Selenzyme is a retrobiosynthesis tool that suggests candidate enzymes for user query reactions. Enzyme suggestions are based on identical reactions, as well as similar reactions, since enzymes are often capable of promiscuous substrate binding. Selenzyme is a user-friendly, widely used web-tool for ranking enzymes based on reaction similarity and additional features, including the phylogenetic distance between the source species of the enzyme and the intended host. While Selenzyme has proved invaluable in assisting with enzyme selection for known reactions, as well as many novel or orphan reactions, weaknesses have been exposed in its ability to rank functionally related enzymes. Within this update, we introduce a new reaction similarity scoring algorithm, which is used in conjunction with the previous similarity calculation, to improve the accuracy of enzyme suggestions based on non-identical similar reactions, across a range of EC reaction classes. This allows enzymes to be suggested for reactions not found within the database, even if the reaction is unbalanced. A database update was also carried out, to ensure that reaction and enzyme knowledge remains current. This update can be accessed at http://selenzymeRF.synbiochem.co.uk/.
Identifiants
pubmed: 38074466
doi: 10.1016/j.csbj.2023.11.039
pii: S2001-0370(23)00454-3
pmc: PMC10697999
doi:
Types de publication
Journal Article
Langues
eng
Pagination
5868-5876Informations de copyright
© 2023 The Authors.
Déclaration de conflit d'intérêts
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
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