Introduction

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

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
  • Chemically-modified macromolecules
• And other related information, such as:
  
  • Genes
  • Proteins
  • Pathways
  • Literature
  • Patents
• and more....

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

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.