SelenzymeRF: updated enzyme suggestion software for unbalanced biochemical reactions
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...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-01-01
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| Series: | Computational and Structural Biotechnology Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037023004543 |
| _version_ | 1797384074561585152 |
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| author | Ruth A. Stoney Erik K.R. Hanko Pablo Carbonell Rainer Breitling |
| author_facet | Ruth A. Stoney Erik K.R. Hanko Pablo Carbonell Rainer Breitling |
| author_sort | Ruth A. Stoney |
| collection | DOAJ |
| description | 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/. |
| first_indexed | 2024-03-08T21:30:15Z |
| format | Article |
| id | doaj.art-8af61ea328b14d9483bf7e2a21b06bbf |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-03-08T21:30:15Z |
| publishDate | 2023-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-8af61ea328b14d9483bf7e2a21b06bbf2023-12-21T07:32:35ZengElsevierComputational and Structural Biotechnology Journal2001-03702023-01-012158685876SelenzymeRF: updated enzyme suggestion software for unbalanced biochemical reactionsRuth A. Stoney0Erik K.R. Hanko1Pablo Carbonell2Rainer Breitling3Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, UKManchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, UKInstitute of Industrial Control Systems and Computing (AI2), Universitat Politècnica de València (UPV), 46022 Valencia, Spain; Institute for Integrative Systems Biology I2SysBio, Universitat de València-CSIC, 46980 Paterna, Spain; Corresponding author at: Institute of Industrial Control Systems and Computing (AI2), Universitat Politècnica de València (UPV), 46022 Valencia, Spain.Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK; Corresponding author.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/.http://www.sciencedirect.com/science/article/pii/S2001037023004543RetrobiosynthesisEnzyme selectionReacting siteReaction similarityUnbalanced reactionsRXNMapper |
| spellingShingle | Ruth A. Stoney Erik K.R. Hanko Pablo Carbonell Rainer Breitling SelenzymeRF: updated enzyme suggestion software for unbalanced biochemical reactions Computational and Structural Biotechnology Journal Retrobiosynthesis Enzyme selection Reacting site Reaction similarity Unbalanced reactions RXNMapper |
| title | SelenzymeRF: updated enzyme suggestion software for unbalanced biochemical reactions |
| title_full | SelenzymeRF: updated enzyme suggestion software for unbalanced biochemical reactions |
| title_fullStr | SelenzymeRF: updated enzyme suggestion software for unbalanced biochemical reactions |
| title_full_unstemmed | SelenzymeRF: updated enzyme suggestion software for unbalanced biochemical reactions |
| title_short | SelenzymeRF: updated enzyme suggestion software for unbalanced biochemical reactions |
| title_sort | selenzymerf updated enzyme suggestion software for unbalanced biochemical reactions |
| topic | Retrobiosynthesis Enzyme selection Reacting site Reaction similarity Unbalanced reactions RXNMapper |
| url | http://www.sciencedirect.com/science/article/pii/S2001037023004543 |
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