UPCMLD BioActivity Database

About the UPCMLD-ChemBioData Database

UPCMLD-ChemBioData is a Web-interfaced meta-database constructed by extracting bioassays data and UPCMLD-related chemical information from the NIH PubChem library. UPCMLD-ChemBioData provides various queries and data-mining functions for UPCMLD users to quickly and easily search for UPCMLD-synthesized chemical compound information and the corresponding bioassay data from the PubChem database (http://pubchem.ncbi.nlm.nih.gov/).  UPCMLD-ChemBioData was developed by Profs. Xie’s and Wipf’s laboratories with a long term objective to develop algorithms and tools to facilitate the research of UPCMLD chemists and the broader scientific community interested in Diversity–Oriented Synthesis. UPCMLD-ChemBioData enables the development and improvement of chemically and biologically important probe molecules from the NIH SMR repository. UPCMLD-ChemBioData can therefore also prove useful for new drug development.

UPCMLD-ChemBioData has currently the following query functions:

  • Text query function: searches by PI Name, UPCMLD Name, or compound physical properties (MW, Formula, clogP, HA, HD, etc).
  • Structure query function:  substructure search and similarity search of whole UPCMLD compounds or the active UPCMLD compounds.
  • Biodata query: Search all bioactivity data in PubChem bioassays for a particular UPCMLD compound.
  • BioAssay query function: Search all UPCMLD compounds in a particular bioassay.
  • Full view function: List all the bioactivity values if they were deposited in PubChem, compound ID, PI name, physical and biochemical properties.

As of today, UPCMLD-ChemBioData has a total of 5,820 UPCMLD compounds (CID) that were biologically tested. Among these, 2,340 were listed as “Active” (or confirmed) in 1,649 BioAssays (AID) deposited in the PubChem Database, targeting 453 proteins(or protein complexes) and also different cell lines (updated on July 19, 2011). The UPCMLD-ChemBioData resource is managed and updated regularly by Dr. Lirong Wang (liw30@pitt.edu ) in Prof. Xie’s laboratory (xix15@pitt.edu)  (www.CBLigand.org/xielab ), a member of the UPCMLD.

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(Last updated on Dec, 2009)