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PubChem is an open chemistry database at the National Institutes of Health (NIH), containing mostly small molecules, but also larger molecules such as nucleotides, carbohydrates, lipids, peptides, and chemically-modified macromolecules. PubChem collects information on chemical structures, identifiers, chemical and physical properties, biological activities, patents, health, safety, toxicity data, and many others.
Start at the library home page, and click the Databases tab at left. Click the initial letter of the database you are looking for in the A-Z listing, or browse the titles on the page. Click the name of the database you are looking for.
Kim paper covers the following:
Basic Protocol 1: Finding genes and proteins that interact with a given compound
Basic Protocol 2: Finding drug-like compounds similar to a query compound through a two-dimensional (2-D) similarity search
Basic Protocol 3: Finding compounds similar to a query compound through a three-dimensional (3-D) similarity search
Support Protocol: Computing similarity scores between compounds
Basic Protocol 4: Getting the bioactivity data for the hit compounds from substructure search
Basic Protocol 5: Finding drugs that target a particular gene
Basic Protocol 6: Getting bioactivity data of all chemicals tested against a protein
Basic Protocol 7: Finding compounds annotated with classifications or ontological terms
Basic Protocol 8: Finding stereoisomers and isotopomers of a compound through identity search
The chemical structure of glutathione, an antioxidant that may help resist the toxins that are an underlying cause of aging. (Graphic courtesy of Oregon State University) CC BY SA
The second video demonstrates how to compare two compounds.
