The ChEMBL-og

(Generated with DALL-E 3 ∙ 30 October 2023 at 1:48 pm) We have some very exciting news to report: the new SureChEMBL is now available! Hooray! What is SureChEMBL, you may ask. Good question! In our portfolio of chemical biology services, alongside our established database of bioactivity data for drug-like molecules ChEMBL , our dictionary of annotated small molecule entities ChEBI , and our compound cross-referencing system UniChem , we also deliver a database of annotated patents! Almost 10 years ago , EMBL-EBI acquired the SureChem system of chemically annotated patents and made this freely accessible in the public domain as SureChEMBL. Since then, our team has continued to maintain and deliver SureChEMBL. However, this has become increasingly challenging due to the complexities of the underlying codebase. We were awarded a Wellcome Trust grant in 2021 to completely overhaul SureChEMBL, with a new UI, backend infrastructure, and new f...

  The ChEMBL database contains bioactivity data that links compounds to their biological targets.  Most ChEMBL targets are proteins (~ 70% in version 27) and these are mapped to their UniProt accessions.   On the ChEMBL interface, searches can be performed with either protein names or accessions...but did you know that protein similarity searches are also possible? Here’s an example using human Phospholipase DDHD2 , a target not found in ChEMBL.       1.       On the ChEMBL interface , click 'Enter a Sequence:     2.       Input the FASTA sequence corresponding to human  Phospholipase DDHD2  and click 'Search in ChEMBL':  3.      Review the BLAST results, select targets of interest and browse bioactivity data: The BLAST  search identifies the mouse  Phospholipase DDHD2   homologue alongside a small number of bioactivity data points and active compounds . ChE...

We are pleased to announce that we have a beta version of a new ChEMBL interface that we would like you to try out.  It can be found here   There are also a lot of additional features in the new interface such as free text searching. You no longer need to specify that you want to search for a compound, target, document etc. Also as you type your search, there will be suggestions made for you. You can also filter of results to see just the subset of data you are interested in using a number of different filtering options. However, the new interface still retains some of the old features such as compound and target report cards.  More details on the new features can be found here  and we have also updated our FAQs.  But most of all we hope it is intuitive to use. It will replace the old interface soon but before we retire the old one we would like some feedback on the new one. We will continue to evol...

Previously in the SureChEMBL series, we described how to access SureChEMBL data in bulk , offline and locally. So, you may ask, what is the point in using the SureChEMBL web interface ? Well, how about the unprecedented functionality that allows you to submit very granular queries by combining: i) Lucene fields against full-text and bibliographic metadata and ii) advanced structure query features against the annotated compound corpus - at the same time? Let’s see each one separately first: Lucene-powered keyword searching You may use the main text box for simple keyword-based patent searches, such as ‘Apple’, ‘diabetes’ or even ' chocolate cake ' (the patent corpus as a recipe book is a new use-case here). You will get a lot of results and probably a lot of noise. With Lucene fields, you can slice and dice a query by indicating specific patent sections and bibliographic metadata, such as date/year of filing or publication, assignee, patent classification code,...