Skip to main content

ChEMBL 26 Released

By


We are pleased to announce the release of ChEMBL_26

This version of the database, prepared on 10/01/2020 contains:

  • 2,425,876 compound records
  • 1,950,765 compounds (of which 1,940,733 have mol files)
  • 15,996,368 activities
  • 1,221,311 assays
  • 13,377 targets
  • 76,076 documents
You can query the ChEMBL 26 data online via the ChEMBL Interface and you can also download the data from the ChEMBL FTP site. Please see ChEMBL_26 release notes for full details of all changes in this release.

Changes since the last release:

* Deposited Data Sets:

CO-ADD antimicrobial screening data:
Two new data sets have been included from the Community for Open Access Drug Discovery (CO-ADD). These data sets are screening of the NIH NCI Natural Product Set III in the CO-ADD assays (src_id = 40, Document ChEMBL_ID = CHEMBL4296183, DOI = 10.6019/CHEMBL4296183) and screening of the NIH NCI Diversity Set V in the CO-ADD assays (src_id = 40, Document ChEMBL_ID = CHEMBL4296182, DOI = 10.6019/CHEMBL4296182).

HESI - Evaluation of the utility of stem-cell derived cardiomyocytes for drug proarrhythmic potential (src_id = 49, Document ChEMBL_ID = CHEMBL4295262 , DOI = 10.6019/CHEMBL4295262). Summary assay results for this data set have been included in ChEMBL_26 and further supplementary data will be added in ChEMBL_27.

* Changes to structure-processing and compound properties:
We are now using RDKit for almost all of our compound-related processing. For the first time in ChEMBL_26, this will include compound standardization, salt-stripping, generation of canonical smiles, structural alerts, image depiction, substructure searches and similarity searches (via FPSim2: https://github.com/chembl/FPSim2). Therefore, all molecules have been reprocessed and you may notice some differences in molfiles, smiles and structure search results compared with previous releases. The ChEMBL structure curation pipeline has been released as an open source package: https://github.com/chembl/ChEMBL_Structure_Pipeline, and incorporated into our Beaker web services (see below). More information can be found here: http://chembl.blogspot.com/2020/02/chembl-compound-curation-pipeline.html.

We are also now using ChemAxon tools to calculate most acidic and basic pKa, logP and logD (pH 7.4) predictions, rather than ACDLabs software. These properties have therefore been recalculated and renamed in the database.

* Target Predictions:
Target predictions in ChEMBL are now generated by a new method, using conformal prediction (https://jcheminf.biomedcentral.com/articles/10.1186/s13321-018-0325-4). A docker image is available for those wishing to use the models locally: https://hub.docker.com/repository/docker/chembl/mcp (see https://chembl.blogspot.com/2020/01/new-chembl-ligand-based-target.html for more information). We also plan to provide a new target prediction web service in the future. The current target prediction web service (https://www.ebi.ac.uk/chembl/api/data/target_prediction/) has now been deprecated.

* Updated Data Sets:
Scientific Literature
Patent Bioactivity Data
Orange Book
USP Dictionary of USAN and International Drug Names
Clinical Candidates
WHO Anatomical Therapeutic Chemical Classification
British National Formulary
Manually Added Drugs

Database changes:

# Columns Added:

CELL_DICTIONARY
CELL_ONTOLOGY_ID VARCHAR2(10) ID for the corresponding cell type in the Cell Ontology

VARIANT_SEQUENCES
TAX_ID   NUMBER(11,0) NCBI Tax ID for the organism from which the sequence was obtained

COMPOUND_PROPERTIES
CX_MOST_APKA NUMBER(9,2) The most acidic pKa calculated using ChemAxon v17.29.0
CX_MOST_BPKA NUMBER(9,2) The most basic pKa calculated using ChemAxon v17.29.0
CX_LOGP NUMBER(9,2) The calculated octanol/water partition coefficient using ChemAxon v17.29.0
CX_LOGD NUMBER(9,2) The calculated octanol/water distribution coefficient at pH7.4 using ChemAxon v17.29.0

# Columns Removed:

COMPOUND_PROPERTIES
ACD_MOST_APKA Replaced by CX_MOST_APKA
ACD_MOST Replaced by CX_MOST_BPKA
ACD_LOGP Replaced by CX_LOGP
ACD_LOGD Replaced by CX_LOGD


Funding acknowledgements:

Work contributing to ChEMBL26 was funded by the Wellcome Trust, EMBL Member States, Open Targets, National Institutes of Health (NIH), EU Innovative Medicines Initiative 2 (IMI2) and EU Horizon 2020 programmes. Please see https://chembl.gitbook.io/chembl-interface-documentation/acknowledgments for more details.


If you require further information about ChEMBL, please contact us: chembl-help@ebi.ac.uk

# To receive updates when new versions of ChEMBL are available, please sign up to our mailing list: http://listserver.ebi.ac.uk/mailman/listinfo/chembl-announce
# For general queries/feedback please email: chembl-help@ebi.ac.uk
# For details of upcoming webinars, please see: http://chembl.blogspot.com/search/label/Webinar
Labels:

Comments

Post a Comment

Popular posts from this blog

ChEMBL 34 is out!

By
We are delighted to announce the release of ChEMBL 34, which includes a full update to drug and clinical candidate drug data. This version of the database, prepared on 28/03/2024 contains:         2,431,025 compounds (of which 2,409,270 have mol files)         3,106,257 compound records (non-unique compounds)         20,772,701 activities         1,644,390 assays         15,598 targets         89,892 documents Data can be downloaded from the ChEMBL FTP site:  https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_34/ Please see ChEMBL_34 release notes for full details of all changes in this release:  https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_34/chembl_34_release_notes.txt New Data Sources European Medicines Agency (src_id = 66): European Medicines Agency's data correspond to EMA drugs prior to 20 January 2023 (excluding vaccines). 71 out of the 882 newly added EMA drugs are only authorised by EMA, rather than from other regulatory bodies e.g.
Post a Comment
Read more

New SureChEMBL announcement

By
(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
Post a Comment
Read more

Accessing SureChEMBL data in bulk

By
It is the peak of the summer (at least in this hemisphere) and many of our readers/users will be on holiday, perhaps on an island enjoying the sea. Luckily, for the rest of us there is still the 'sea' of SureChEMBL data that awaits to be enjoyed and explored for hidden 'treasures' (let me know if I pushed this analogy too far). See here and  here for a reminder of SureChEMBL is and what it does.  This wealth of (big) data can be accessed via the SureChEMBL interface , where users can submit quite sophisticated and granular queries by combining: i) Lucene fields against full-text and bibliographic metadata and ii) advanced structure query features against the annotated compound corpus. Examples of such queries will be the topic of a future post. Once the search results are back, users can browse through and export the chemistry from the patent(s) of interest. In addition to this functionality, we've been receiving user requests for  local (behind the
Post a Comment
Read more

Mapping lists of IDs in ChEMBL

By
In order to facilitate the mapping of identifiers in ChEMBL, we have developed a new type of search in the ChEMBL Interface. Now, it is possible to enter a list of ChEMBL IDs and see a list of the corresponding entities. Here is an example: 1. Open the ChEMBL Interface , on the main search bar, click on 'Advanced Search': 2. Click on the 'Search by IDs' tab: 3. Select the source entity of the IDs and the destination entity that you want to map to: 4. Enter the identifiers, you can either paste them, or select a file to upload. When you paste IDs, by default it tries to detect the separator. You can also select from a list of separators to force a specific one: Alternatively, you can upload a file, the file can be compressed in GZIP and ZIP formats, this makes the transfer of the file to the ChEMBL servers faster. Examples of the files that can be uploaded to the search by IDs can be found  here . 5. Click on the search button: 6. You will be redirected to a search resul
Post a Comment
Read more

New Drug Approvals - Pt. XVII - Telavancin (Vibativ)

By jpo
The latest new drug approval, on 11th September 2009 was Telavancin - which was approved for the treatment of adults with complicated skin and skin structure infections (cSSSI) caused by susceptible Gram-positive bacteria , including Staphylococcus aureus , both methicillin-resistant (MRSA) and methicillin-susceptible (MSSA) strains. Telavancin is also active against Streptococcus pyogenes , Streptococcus agalactiae , Streptococcus anginosus group (includes S. anginosus, S. intermedius and S. constellatus ) and Enterococcus faecalis (vancomycin susceptible isolates only). Telavancin is a semisynthetic derivative of Vancomycin. Vancomycin itself is a natural product drug, isolated originally from soil samples in Borneo, and is produced by controlled fermentation of Amycolatopsis orientalis - a member of the Actinobacteria . Telavancin has a dual mechanism of action, firstly it inhibits bacterial cell wall synthesis by interfering with the polymerization and cross-linking of peptid
Post a Comment
Read more