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In an NMR sample, precise measurement of the absolute absorption frequencies of nuclei is difficult. A standard internal reference compound is added, and the frequency difference between the reference signal and sample signals is measured.
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Exploring Chemical Information in PubChem.

Sunghwan Kim1

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland.

Current Protocols
|August 9, 2021
PubMed
Summary
This summary is machine-generated.

PubChem is a public chemical database that links various data collections, enabling users to find interactions between chemicals, genes, and proteins. This guide provides instructions for exploring PubChem data, including structure and similarity searches.

Keywords:
PubChemchemical structure searchcheminformaticsdrug discoverymolecular similaritypublic database

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Area of Science:

  • Biochemistry
  • Cheminformatics
  • Drug Discovery

Background:

  • PubChem is a comprehensive public chemical database.
  • It integrates diverse data collections such as Substance, Compound, BioAssay, Protein, Gene, Pathway, and Patent.
  • These collections are interconnected, facilitating the discovery of relationships between chemical entities and biological targets.

Purpose of the Study:

  • To provide a guide for exploring PubChem data.
  • To demonstrate how to perform various searches, including keyword and chemical structure searches.
  • To illustrate common tasks such as finding interacting genes and proteins, identifying similar compounds, and retrieving bioactivity data.

Main Methods:

  • Keyword searches for chemicals, proteins, or genes.
  • Chemical structure searches using line notations or the PubChem Sketcher.
  • Support for identity, 2-D/3-D similarity, substructure, and superstructure searches.
  • Boolean operators for complex query formulation.
  • Retrieval of records based on classification or ontological terms.

Main Results:

  • Step-by-step instructions for 8 basic protocols are provided.
  • Protocols cover finding gene/protein interactions, drug-like compounds, bioactivity data, and target drugs.
  • Methods for similarity scoring and identifying stereoisomers/isotopomers are included.

Conclusions:

  • PubChem is a versatile resource for scientific research and public information.
  • The provided protocols enable efficient data exploration and retrieval.
  • Users can leverage PubChem for tasks ranging from basic compound identification to complex bioactivity analysis.