Search chemical structure

Structure databases are databases that contain information on chemical structures and compounds. The compounds or structure diagrams are not stored as graphics but are represented as connection tables (see Section 2.4). The information about the structure includes the topological arrangement of atoms and the connection between these atoms. This strategy of storage is different from text files and allows one to search chemical structures in several ways. 

In the previous chapter, we learnt the use of fingerprints for searching chemical structures. Of equal importance is the need for searching chemical reactions to estimate their similarity using computational tools. In this section, we will therefore learn how to use reaction fingerprints for searching in databases and online servers. Similar techniques are employed in both cases. Stractural properties that are present in the reaction are used for estimation of reaction similarity. Two reactions can be considered similar if their product side artd/or reactant side are similar. With this consideration, reaction sirrrilarity is reduced to molecular or 5irMctMro/ similarity. 

One final note, the SQ program is actually a hybrid that utilizes both graph theoretic and regional approaches to perform molecular superpositions in a computationally efficient manner. Its objective nature and inherent speed make it suitable for comparing molecules that vary greatly in shape, size, and composition and it has been used to search chemical structure databases. 

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