Frequently Asked Questions

How is the EnzymePortal 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 EP pages and refer to the information in the underlying primary database (Uniprot, PDB, etc.) directly.

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

What is the meaning of those compounds used as filters for the search results?

The compounds listed along the search results are any small molecules which are related to them, be it as reactants, products, activators, inhibitors or cofactors of those enzymes. They can be used as filters to narrow your search if you are particularly interested in the biochemistry of concrete chemicals, for example enzymes using manganese as a cofactor.

What are the figures in colourful labels which appear with the results of a protein sequence search?

The figures are bit scores for the blast search of the given sequence against the shown enzyme. The colour is a hint for the match: red means a close match, blue a loose one. It helps to locate best results at first sight.

For more information about scores, please refer to the BLAST documentation.

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

The small molecules tab shows any bioactive compounds described in ChEMBL as interacting with the enzyme. The link See all bioactive compounds in ChEMBL will take 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 can I combine search filters?

Search results can be filtered using the facets shown on the left hand side in three blocks: species, chemical compounds 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.