Database Update March 2015

The latest GtoPdb update was released on March 13th and this first release of 2015 includes major updates in several areas.

GPCR updates:

Kinase updates

  • Added affinity data (where available) for all of the kinase inhibitors in the database (including those we previously only had large-scale matrix screening data for), tagging primary targets where appropriate
  • Also added information for kinase inhibitors in clinical trials

Epigenetics target updates

Protease updates

  • This target class now includes a first (for the database) with a predrug > prodrug > drug triplet. These were curated from a paper describing how MMP12 produces its own inhibitor in a two-step activation procedure. We now have ligand entries for the peptide substrate of the protease, the prodrug and the drug.

Ligand updates

  • More than 420 new ligands added in this release.
  • Many new kinase inhibitors
  • New monoclonal antibodies and small molecules included in pharma pipelines (including any novel drug targets)
  • Sourced available binding affinity data for all monoclonal antibodies in the database using a combination of BLAST sequence analysis, patent and literature searches, tagging primary targets as appropriate
  • More than 20 compounds annotated with new/expanded drug approval information

Disease information updated

  • Target pathophysiology sections have been updated with standardised disease nomenclature
  • Disease name synonyms added
  • More links added to the OMIM and Orphanet disease databases
  • Added Disease Ontology nomenclature and links to the Ontobee disease ontology browser

Website updates

  • New “Specialist databases” section created to highlight database links that are of particular interest on specific target and ligand pages, for example the IMGT/mAb-DB resource for antibodies

Ligand search tools

  • Our chemical structure search tool now uses the Marvin JS structure editor from ChemAxon, which replaces the older Java version. The new JavaScript version has the advantage of cross-platform compatibility
  • This version should also be compatible with tablets and mobile devices
  • Useful features include the ability to import molecules through various file formats, structural identifiers or by compound name
  • Compounds can also be exported in many different formats or as an image file

As always, updated data files are available to download with all the new data.

Posted in Database updates

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