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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.
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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