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Introduction

Description of PubChem Workshop

Today's Workshop:

  • Background on the PubChem Project & Databases
  • Searching in PubChem with text or structures
  • Finding molecular & chemical safety information
  • Finding a potential inhibitor for your protein
(full set of workshop slides)



A button to download the slides in PDF format for this section

What is PubChem?

  • Created in 2004 to serve as a repository for the NIH Molecular Libraries Program
  • World's largest collection of freely accessible chemical information
  • Key chemical information resource for scientists, students, and the public


What is in PubChem?

  • Small molecules
  • Larger molecules, such as nucleotides, carbohydrates, lipids, peptides, and chemically-modified macromolecules
  • And other related information, such as genes, proteins, pathways, literature, patents,and more....
How much data is in PubChem?   Click here to see!


Why do people use PubChem data?

  • Learn about a chemical or drug/medication
  • Find chemical and physical properties, molecular structure, chemical safety data, etc.
  • Identify sources of informaton about biological function and other data for fundamental research
  • Mine data for biochemical research
    • Drug discovery, drug-gene targeting, toxicology


Description of PubChem data sources

Where does PubChem's data come from?

  • Vetted Submitters and Contributors who submit data to us or permit us to pull data from their resources, respectively.
  • To learn more, take a look at this Data Sources site.
  • Do you have chemical or biological activity data to contribute?  Learn more here.



How are PubChem's main databases organized?

  • Primary databases:
    • PubChem Substance - depositor-provided information (names, structures, sometimes more)
    • PubChem BioAssay - depositor-provided biological activity experiments (metadata and data) which have been provided with their corresponding tested substances in the PubChem Substance database
  • The main Chemical database:
    • PubChem Compound - non-redundant, aggregate data (based on identical 2D-chemical structures) created by NCBI of PubChem Substance information as well as other relevant data from Contributors.
  • All databases contain links to related records within each database and to relevant records in other PubChem and NCBI molecular biology and literature databases.
Info & Relationship of PubChem's 3 major databases.




PubChem's Homepage

Where do you start?

  • On the PubChem Homepage!
  • To learn more about PubChem:  click on About
  • For chemical information:  look in PubChem Compound
  • For biological activity experiment information:  look in PubChem BioAssay

Last Reviewed: June 5, 2023