Wanted: Experienced Java Developer

We are looking for an experienced Java developer/contractor to work with us on a really innovative text-mining and Java backend development project, related to SureChEMBL and the Illuminating the Druggable Genome (IDG) grant.

The role will be on a 6-month contract and will involve the development of new Java components for the extraction, storage and provision of biological named entities in patent documents.

The suitable candidate (like Alice above) will have more than three years hands-on experience working as an Enterprise Java Developer in production environments with large codebases. Experience in the field of chemo/bioinformatics would be ideal but not a a deal-breaker.

More information on the job description and requirements here.

If you think you have what it takes, drop us a line with your CV.

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Here's a nice Christmas gift - ChEMBL 35 is out!

Use your well-deserved Christmas holidays to spend time with your loved ones and explore the new release of ChEMBL 35! This fresh release comes with a wealth of new data sets and some new data sources as well. Examples include a total of 14 datasets deposited by by the ASAP ( AI-driven Structure-enabled Antiviral Platform) project, a new NTD data se t by Aberystwyth University on anti-schistosome activity, nine new chemical probe data sets, and seven new data sets for the Chemogenomic library of the EUbOPEN project. We also inlcuded a few new fields that do impr ove the provenance and FAIRness of the data we host in ChEMBL: 1) A CONTACT field has been added to the DOCs table which should contain a contact profile of someone willing to be contacted about details of the dataset (ideally an ORCID ID; up to 3 contacts can be provided). 2) In an effort to provide more detailed information about the source of a deposited dat...

Improvements in SureChEMBL's chemistry search and adoption of RDKit

Dear SureChEMBL users, If you frequently rely on our "chemistry search" feature, today brings great news! We’ve recently implemented a major update that makes your search experience faster than ever. What's New? Last week, we upgraded our structure search engine by aligning it with the core code base used in ChEMBL . This update allows SureChEMBL to leverage our FPSim2 Python package , returning results in approximately one second. The similarity search relies on 256-bit RDKit -calculated ECFP4 fingerprints, and a single instance requires approximately 1 GB of RAM to run. SureChEMBL’s FPSim2 file is not currently available for download, but we are considering generating it periodicaly and have created it once for you to try in Google Colab ! For substructure searches, we now also use an RDKit -based solution via SubstructLibrary , which returns results several times faster than our previous implementation. Additionally, structure search results are now sorted by...

ChEMBL 34 is out!

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Improved querying for SureChEMBL

Dear SureChEMBL users, Earlier this year we ran a survey to identify what you, the users, would like to see next in SureChEMBL. Thank you for offering your feedback! This gave us the opportunity to have some interesting discussions both internally and externally. While we can't publicly reveal precisely our plans for the coming months (everything will be delivered at the right time), we can at least say that improving the compound structure extraction quality is a priority. Unfortunately, the change won't happen overnight as reprocessing 167 millions patents takes a while. However, the good news is that the new generation of optical chemical structure recognition shows good performance, even for patent images! We hope we can share our results with you soon. So in the meantime, what are we doing? You may have noticed a few changes on the SureChEMBL main page. No more "Beta" flag since we consider the system to be stable enough (it does not mean that you will never ...

ChEMBL brings drug bioactivity data to the Protein Data Bank in Europe

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