An update on the Enzyme Portal: an integrative approach for exploring enzyme knowledge

Pundir, Sangya; Onwubiko, Joseph; Zaru, Rossana; Rosanoff, Steven; Antunes, Ricardo; Bingley, Megan; Watkins, Xavier; O′Donovan, Claire; Martin, Maria Jesus

doi:10.1093/protein/gzx008

Cited by 13 publications

(10 citation statements)

References 14 publications

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“…Pundir et al reported that plant enzymes are effective in reducing the risk of cancer [8]. Similarly to the results of this study, plant enzymes are thought to exhibit antitumor effects by mediating the activity of immune cells [8–10].…”

Section: Discussionsupporting

confidence: 71%

Plant Enzymes Decrease Prostate Cancer Cell Numbers and Increase TNF-α In Vivo: A Possible Role in Immunostimulatory Activity

Yamashita

Yamamoto

et al. 2019

International Journal of Food Science

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Increased caloric intake and Westernized dietary choices may be contributing toward a recent rising trend of incidences of chronic lifestyle-related diseases. In this study, we evaluated the anticancer properties of Plant Enzyme Validux (PEV) using a mouse model. Five-week-old male C3H mice were randomly distributed into four experimental groups: Control, PEV only, 6Gy irradiation only, and PEV + 6Gy. PEV was orally administered daily at 500 mg/kg for 14 days prior to three rounds of 2Gy irradiation. We focused on the anticancer action and immunostimulatory effects of PEV with and without irradiation. Oncogene suppression was observed after PEV treatment as was an increase in TNF-α, suggesting an antitumor effect. PEV administration also appeared to reduce oxidative stress as evidenced by a decrease in lipid peroxidation. In addition, PEV confirmed radioprotective effect by radical blocking ability by radiation irradiation. Immunological responses to PEV administration were evidenced by an increase in number of total white blood cells and T lymphocytes. Immunotherapy is drawing more and more attention as a treatment for prostate cancer, suggesting that there will be a need for the identification of specific targets for prostate cancer and for more basic research on the genetic aspects of immunotherapy. Thus, PEV may be of use as a radioprotective supplement during radiotherapy for tumor treatment.

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Section: Discussionsupporting

confidence: 71%

Plant Enzymes Decrease Prostate Cancer Cell Numbers and Increase TNF-α In Vivo: A Possible Role in Immunostimulatory Activity

Yamashita

Yamamoto

et al. 2019

International Journal of Food Science

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“…Several annotations for a sequence can now be recognized more easily by the number in the circle behind the given UniProt Sequence ID. There are also additional external links for each prediction to the EBI Enzyme Portal ( 33 ), KEGG, PATRIC, BrEPS, the best BLAST hit, BKMS-react, InterPro ( 34 ) and MMTB. The Metano Modeling Toolbox (MMTB) is an online tool based on the data of BKMS-react that assists metabolic modeling by providing an interface to the Metano software ( 35 ).…”

Section: New Developments and Major Improvementsmentioning

confidence: 99%

BRENDA, the ELIXIR core data resource in 2021: new developments and updates

Chang

Jeske

Ulbrich

et al. 2020

Nucleic Acids Research

501

349

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The BRENDA enzyme database (https://www.brenda-enzymes.org), established in 1987, has evolved into the main collection of functional enzyme and metabolism data. In 2018, BRENDA was selected as an ELIXIR Core Data Resource. BRENDA provides reliable data, continuous curation and updates of classified enzymes, and the integration of newly discovered enzymes. The main part contains >5 million data for ∼90 000 enzymes from ∼13 000 organisms, manually extracted from ∼157 000 primary literature references, combined with information of text and data mining, data integration, and prediction algorithms. Supplements comprise disease-related data, protein sequences, 3D structures, genome annotations, ligand information, taxonomic, bibliographic, and kinetic data. BRENDA offers an easy access to enzyme information from quick to advanced searches, text- and structured-based queries for enzyme-ligand interactions, word maps, and visualization of enzyme data. The BRENDA Pathway Maps are completely revised and updated for an enhanced interactive and intuitive usability. The new design of the Enzyme Summary Page provides an improved access to each individual enzyme. A new protein structure 3D viewer was integrated. The prediction of the intracellular localization of eukaryotic enzymes has been implemented. The new EnzymeDetector combines BRENDA enzyme annotations with protein and genome databases for the detection of eukaryotic and prokaryotic enzymes.

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“…ChEMBL ( 19 ) and MEROPS ( 20 ), ENA Barcode, Geospatial and non-coding sequences ( 11 ), have been added to the sequence similarity search libraries. Importantly, new UniProt Reference Proteomes ( 13 ) and Enzyme Centric ( 21 ) libraries are also now available.…”

Section: New Analysis Tools and Databasesmentioning

confidence: 99%

Programmatic access to bioinformatics tools from EMBL-EBI update: 2017

Chojnacki

Cowley

Lee

et al. 2017

Nucleic Acids Research

284

210

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Since 2009 the EMBL-EBI provides free and unrestricted access to several bioinformatics tools via the user's browser as well as programmatically via Web Services APIs. Programmatic access to these tools, which is fundamental to bioinformatics, is increasingly important as more high-throughput data is generated, e.g. from proteomics and metagenomic experiments. Access is available using both the SOAP and RESTful approaches and their usage is reviewed regularly in order to ensure that the best, supported tools are available to all users. We present here an update describing the latest enhancement to the Job Dispatcher APIs as well as the governance under it.

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An update on the Enzyme Portal: an integrative approach for exploring enzyme knowledge

Cited by 13 publications

References 14 publications

Plant Enzymes Decrease Prostate Cancer Cell Numbers and Increase TNF-α In Vivo: A Possible Role in Immunostimulatory Activity

Plant Enzymes Decrease Prostate Cancer Cell Numbers and Increase TNF-α In Vivo: A Possible Role in Immunostimulatory Activity

BRENDA, the ELIXIR core data resource in 2021: new developments and updates

Programmatic access to bioinformatics tools from EMBL-EBI update: 2017

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