Frequently Asked Questions

How is the Enzyme Portal different from BRENDA?

The EnzymePortal is a one-stop shop for enzyme-related information in resources developed at the EBI. It accumulated this information and aims to present it to the scientist with a unified user experience. The EnzymePortal team does not curate enzyme information and therefore is a secondary information resource or portal. At some point, a user interested in more detail will always leave the Enzyme Portal pages and refer to the information in the underlying primary database (UniprotKB, PDB, etc.) directly.

BRENDA is the most comprehensive resource about enzymes worldwide and has invested a great amount into the abstraction and curation about enzymes and their related information. BRENDA contains valuable information that cannot be found in the EnzymePortal at the moment, such as kinetic, specificity, stability, application, and disease-related data. As a primary resource, BRENDA could be a candidate for an information source for the EnzymePortal in the future.

How can I see species-related information for a given enzyme?

When enzymes have identical name but belong to different species they are grouped into one entry. To see the information related to one particular species use the drop down menu at the top of the enzyme page. Please see video

How can I combine search filters?

Search results can be filtered using the facets shown on the left hand side in three blocks: organism, enzyme classification, cofactors, inhibitors and diseases. Checking more than one filter in the same block narrows the search to those results matching any of them. Checking filters in different blocks shows only results matching all of them.
For example, if you search for sildenafil and then check the filter Species > Human you will see only the enzymes found in human.

Now, checking an additional species - say Mouse - will restrict the list of results to those found either in human or mouse. If you now select a filter in another block - Chemical compounds > Drug > Sildenafil, for example - the results shown will be those enzymes affected by sildenafil and present in either human or mouse.

What is included in the "small molecules" tab of a protein page?

Small molecules are either activators, inhibitors or cofactors related to an enzyme. In the protein result page, the filters on the left-hand can be used to narrow down the search to specific inhibitors or cofactors.

Why does the small molecules tab show fewer Inhibitors than the ChEMBL page?

The small molecules tab shows any Inhibitors described in ChEMBL as inhibiting the enzyme. The link See all inhibitors in ChEMBL will link to a ChEMBL page where you may see many more. The difference is due to a filter applied by the Enzyme Portal, whereby only those compounds more likely to have a significative activity on the function of the enzyme are shown.

How to use the "Browse by" on the home page?

The "Browse by" section in the home page allows to search for enzymes focusing on specific enzyme-related information. For example, you can click on "Disease" and view a list of all diseases that have enzymes linked to them in Enzyme Portal. You can also search for your disease of interest within this list. Clicking on a disease name will take you to a results page listing all enzymes related to that disease. You can explore data in similar ways through the "Enzyme Classification", "Taxonomy" and "Pathways" "Enzyme families", "Cofactors" and "Metabolites" boxes.

How can I search for a disease or a pathway that is not displayed on the Disease or Pathways pages?

The Disease or Pathways pages display only a limited list of the diseases or pathways available in alphabetical order. To search for a disease or a pathway that is not displayed on the page, use the search box on the top of the page. The search box uses a controlled vocabulary. Just start typing the first few letters of the disease or pathway and a drop down menu will appear where the most relevant suggestion can be selected.

Are all species available from the "Taxonomy" page?

Model organisms of major taxa such as Homo sapiens or Escherichia coli are directly available from the taxonomy home page. Other organisms can be found using the search box. By typing the first few letters of a species name, a drop-down menu will appear where the most relevant suggestion can be selected.

What can do I with enzymes in my basket?

The Enzyme Portal basket offers a tool to compare two enzymes. Just select your enzymes of interest and add them to your basket. Once inside your basket, select an organism for the enzymes you wish to compare using the dropdowns under the button called "Compare selected". Then click on the button to compare the selected enzymes. The results will show you a comparison of the content for each enzyme, a comparison of their structures (if available) and a button to launch a comparison of the protein sequences.

Can I download the results from the search?

Yes, You can download search results and in several formats. The download will be a zipped file by default but you can de-select this option using the provided checkbox.

Where can I find reaction parameters such as Michaelis-Menten kinetic parameters?

In the enzyme page, you can find Km/kcat values as well as information about the pH and temperature that have been extracted from the enzyme database BRENDA. For more details follow the link to the corresponding BRENDA page.

In the protein page, you can find similar information (KM, Vmax, pH and temperature) but related to a specific protein entry. This information is extracted from the UniProt database.