The following paper provides step-by-step instructions on how to explore data contained in PubChem, along with examples of commonly requested tasks.
[PubMed PMID: 34370395] [PubMed Central PMCID: PMC8363119] [Free Full Text]
This paper includes several protocols designed to help users to get familiar with PubChem's data and tools.
- 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
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