Judith Currano, Chemistry Librarian at the University of Pennsylvania, notes that searching by substructure is akin to searching text using truncation. ". . . one enters a portion of a molecule into the search system and retrieves substances that contain that fragment, or 'substructure'." (2014, p114)
Currano points out that the challenge to searching by substructure is developing a structure with an appropriate degree of specificity. Depending on your goal, determines how detailed you draw the substructure and she notes that the art of substructure searching comes from "balancing the length of time spent constructing a search with the length of time one wants to spend evaluating the results (2014, p.115)" while a second challenge is guessing how the structure has been represented in the database (p.115).
Currano offers the following steps as a basic procedure for substructure searching:
- identify the portion of the molecule that is of interest.
- determine whether the stereochemistry, geometry, and bond order of each connection in the stucture is fixed or flexible.
- decide where and how your substructure may be further substituted.
- determine the topology of each atom and connection in the structure (p115).
She advises that the searcher to think like a database, rather than as a chemist and to think your structure through before beginning to draw it.
For more detailed information on thinking about and drawing substructures, see Chapter 5 of Chemical Information for Chemists: A primer.
Currano, J. (2014). Searching by structure and substructure. In J.N.Currano & D.L. Roth (Eds.), Chemical Information for Chemists: A primer (pp.109-145). Cambridge,UK: RSC Publishing.