Dear All, I’m excited to share the latest development from our collaborative project between PDBe, CCDC, and ChEMBL -- BioChemGraph.
This project integrates structural, functional, and biochemical data across small molecules and macromolecules, enabling streamlined access to related information from trusted, yet previously disparate datasets. This integration aims to accelerate research in drug discovery, drug repurposing, target validation, and understanding of drug mechanisms by offering comprehensive structural and bioactivity data in one place. ==================================== Key highlights of this BioChemGraph data release: ==================================== (1) Bioactivity Data Integration Over 17,000 protein-ligand complexes from the PDB are now directly linked to 39,000 ChEMBL bioactivity records, which include data on binding affinity, functional assays, inhibition, and more. The bioactivity reports are available in two formats: - bioactivity_report_full.tsv: Detailed ChEMBL records for each protein-ligand complex - bioactivity_report_simple.tsv: Aggregated mean pChEMBL values, offering a standardised measure of compound potency. **The data is updated weekly**, in sync with the PDBe release every Wednesday at 00:00 UTC, and is available for download from our FTP at https://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/additional_data/bioactivity_reports/ (2) CCDC Data Linked via UniChem Over 235,000 CSD identifiers from the Cambridge Structural Database (CSD) are now linked with ChEMBL, PDBe, and other resources via UniChem: https://www.ebi.ac.uk/unichem/ This integration allows researchers to: - Seamlessly explore small-molecule data across diverse resources. - Discover intricate relationships between structural and bioactivity data across platforms, streamlining research and structural analysis. (3) Training Resources Comprehensive training materials are now available at https://colab.research.google.com/drive/16wcovcfn5kBvAdwRT6w3IvYFGqylEebn?usp=sharing This Colab Jupyter Notebook is to help researchers explore and analyse this integrated data. (4) Upcoming Features - PDBe-KB ligand pages will soon be launched, aggregating small-molecule data and provide biological context for small-molecules in the PDB - Residue-level Fragment hotspot maps generated by CCDC for the entire PDB archive will also be integrated into PDBe-KB later this year. ==================================== For more details, please read the full announcement at https://www.ebi.ac.uk/about/news/updates-from-data-resources/biochemgraph-data/ If you have any questions or need assistance navigating the new data, feel free to contact us at pdbeh...@ebi.ac.uk. Best regards, Genevieve Evans Ph.D. PDBe - Protein Data Bank in Europe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK http://www.PDBe.org ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
