ChemicalSearch: Help Notes
Text Search
  • Search Field
  • Search Text
  • Fuzzy Match
  • Structure Search
  • Tversky Parameters
  • Strict Substructure
  • Similarity Threshold
  • Basic Filters
  • SMILES / CDB Chemical ID
  • Molecular Descriptors
  • Sources / Vendors
  • Include Source External IDs
  • Results Limit

  • Text Search
    Search Field Top
    • Select which source / vendor annotation field to perform a text search on. Options include:
    • Chemical name: Any field representing the name of the chemical, systematic or common. For example, find "tylenol" or "acetaminophen," or "serine" or "2-amino-3-hydroxy-propanoic acid"
    • External ID: The ID number / string that the source refers to the chemical as. For example, you could input a CAS registry number or PubChem Substance ID here, and most likely the respective chemical will be found.
    • All annotations: Searches through all of the annotations values, including names, IDs and any other descriptors the sources provide about their chemicals.
    Search Text Top
    • Full-text search of source / vendor annotations, such as chemical names (systematic and common)
    • Powered by the Lucene simple search module, allowing for respective special command characters.
    • The search is case-insensitive and should automatically separate out word components by spaces and punctuation marks.
    Fuzzy Match Top
    • If you are unsure of the spelling for a chemical name, enter your best guess and select the "fuzzy" style search option.
    • This will not only find chemicals with exactly matching name components, but those which are "similar" to the search name.

    Structure Search
    SMILES Top
    • Search for chemicals in the ChemDB with similar structure to a query structure by entering a SMILES string representing the query structure here.
    • Enter multiple SMILES strings (one per line) to perform a profile-based concensus search which searches for items similar to every structure listed. Especially useful when combined with the sub-structure search option to search for chemicals containing several desired functional groups.
    • To sketch a structure instead of specifying a SMILES string, click on the sketch icon. Draw structure
    • To convert various molecular file formats into SMILES, try the online Babel tool.
    • For more information on the de facto standard SMILES string representation, spend a few minutes with the Daylight SMILES Tutorial
    Tversky Parameters Top
    • When performing a similarity search, additional parameters besides the query structure(s) may be specified to fine-tune the query. In particular, the α and β parameters of the Tversky similarity measure may be used to fine-tune the search towards a "super-structure" or "sub-structure" search.
    • For most basic needs, just use the drop-list to select either a Similar or Sub-structure style search which will set reasonable default values for the α and β parameters.
    • The sub-structure search option is especially useful for finding chemicals which possess the query structure as a sub-structure / functional group.
    • For more detailed information on how to use the α and β parameters, refer to the Daylight Tversky Index Description.
    Strict Substructure Top
    • While the similarity α and β parameters can be used to bias towards a sub-structure search, they may still yield some "false positives." That is, structures which have something very similar to the search structures as sub-structures, but not exactly.
    • In combination with substructure biasing α and β parameters, select this option to enforce "strict" substructure searching. Any results returned must have the exact search structures as substructures, not just something "similar."
    Similarity Threshold Top
    • Minimum similarity score that any search results must satisfy for similarity searches.
    • Value should be between 0.0 and 1.0
    • This value is necessary to enable fast similarity searches. A "full" search used to be supported which would not use such a threshold, scanning the entire database for similar molecules. This allowed for the calculation of additional statistics such as a z-score for each result and a similarity distribution histogram and . However, this method would take ~30 seconds per search and has thus since been disabled.

    Basic Filters
    SMILES / CDB Chemical ID Top
    • Search for chemicals having a specific SMILES string or CDB Chemical IDs by selecting one of these from the drop-list.
    • CDB Chemical ID is the numerical identifier used in the ChemDB system to specify every unique chemical.
    • Enter one or more SMILES strings or CDB Chemical IDs (but not both) into the text box, one item per line. Only chemicals which exactly match one of these values will appear in the results.
    • To sketch a chemical structure instead of specifying a SMILES string, click on the sketch icon. Draw structure
    • To convert various molecular file formats into SMILES, try the online Babel tool.
    • For more information on the de facto standard SMILES string representation, spend 15 minutes with the Daylight SMILES Tutorial
    • When searching for chemicals by exact SMILES, as opposed to the similarity search, the match must be exact with what is stored in the database.
    • The database only stores the canonical SMILES (OEChem implementation) for each chemical, thus, arbitrarily constructed SMILES entered into the search field are unlikely to match any canonical SMILES, however...
    • The system will automatically convert your entered SMILES into canonical SMILES representations before searching for exact matches in the database.
    Molecular Descriptors Top
    • To search for chemicals by molecular descriptors, select the descriptors from the drop-lists.
    • Enter a lower-limit (inclusive) and upper-limit (exclusive) for the descriptor.
    • Note that multiple descriptor drop-lists and limit fields are provided to allow for the specification of multiple filters simultaneously ("and" logic).
    • If no limit values are specified, all possible values will be accepted.
    • The chemical search results will include the values for all descriptors selected (whether or not limit values are actually provided).
    • Current descriptors include
      Descriptor Description Source
      Molecular Weight Sum of average atomic weights. OEChem
      Heavy Atoms Number of non-hydrogen atoms. OEChem
      Carbons, Nitrogens, Oxygens Number of respective atoms. OEChem
      XLogP Predicted octanol-water partition coefficient, used to infer permeability through biological membranes. XLogP
      LogP (Chemaxon) Another predicted log P value. ChemAxon Calculator Plugin
      Rotatable Bonds Number of "single, non-ring bond[s] between two non-terminal, non-triple-bonded atoms." Reflects molecular "flexibility." OEChem
      H-Bond Donors Number of Lipinski H-bond donors, simply defined as any hydrogens attached to a nitrogen or oxygen. OEChem
      H-Bond Acceptors Number of Lipinski H-bond acceptor, simply defined as any nitrogens or oxygens. OEChem
      Chiral Atoms Number of chiral atoms / stereocenters. That is, an atom with ≥ 4 distinct neighbors such that different connection arrangements cannot be achieved by simply rotating about the atom. OEChem
      Chiral Bonds Number of chiral bonds. In particular, double bonds with distint constituent pairs at both ends such that rotating about the bond would yield a different configuration. OEChem
      Rigid Segments Number of rigid segments. That is, segments containing no rotatable bonds or segments delimited by rotatable bonds. OEChem
      Solvation Energy ZAP
      Solvation Area ZAP
      Solvation Total ZAP
      Solvation Coulombic ZAP
      3D Coordinates Predicted 3D atom coordinate geometry including isomer enumeration. Not a searchable descriptor, but available for download and usage from chemical isomer downloads. Corina
    Sources / Vendors Top
    • Restrict search results to only include chemicals provided by the selected sources / vendors.
    • Select and deselect multiple sources by performing "Ctrl+Click."
    • Refer to the source / vendor information table to translate source abbreviations into their full names, including company websites where available.

    Include Source External IDs Top
    • Select this option if you want the results to include for each chemical a list of all sources that have it and the external ID number that they refer to it as.
    • In some cases, leaving this option off can significantly improve search times.
    • These and more details for any individual chemical can always be accessed by clicking on the respective chemical link in the results.
    Results Limit Top
    • Set this value to determine the maximum number of results to show per page.
    • Subsequent records can be retrieved using the "Next Page" button in the results section.
    • To protect system performance, this number may not be set to a value > 100.