Chemical File Format - Sources of Chemical Data

Sources of Chemical Data

Here is a short list of sources of freely available molecular data. There are many more resources than listed here out there on the Internet. Links to these sources are given in the references below.

  1. The US National Institute of Health PubChem database is a huge source of chemical data. All of the data is in two-dimensions. Data includes SDF, SMILES, PubChem XML, and PubChem ASN1 formats.
  2. The worldwide Protein Data Bank (wwPDB) is an excellent source of protein and nucleic acid molecular coordinate data. The data is three-dimensional and provided in Protein Data Bank (PDB) format.
  3. eMolecules is a commercial database for molecular data. The data includes a two-dimensional structure diagram and a smiles string for each compound. eMolecules supports fast substructure searching based on parts of the molecular structure.
  4. ChemExper is a commercial data base for molecular data. The search results include a two-dimensional structure diagram and a mole file for many compounds.
  5. New York University Library of 3-D Molecular Structures.
  6. The US Environmental Protection Agency's The Distributed Structure-Searchable Toxicity (DSSTox) Database Network is a project of EPA's Computational Toxicology Program. The database provides SDF molecular files with a focus on carcinogenic and otherwise toxic substances.

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