Pfizer Similarity Searching

The concept of molecular similarity calculation within chemical information systems was pioneered at Sheffield University and first introduced into operational systems at Pfizer Central Research (UK) " and Lederle . It is now well-established within chemical information systems, both commercially available and developed in-house, as described in other papers in this volume. It is a powerful concept, which may be applied to both 2-D and 3-D structural representations, and to chemical reaction information, and used to support similarity searching and browsing, and file clustering and partitioning. 

ChemSelect AQB (Advanced Query Builder) A Pfizer in-house developed reusable Java component that allows users to query various molecular structure databases within Pfizer based on molecular structural information and/or other properties, retrieve, manage, and export retrieved hits. It has a functional role similar to MDL ISIS/BASE, but with many enhanced capabilities. PGVL Hub has embedded this reusable Java component within itself so that users can search for suitable reactants from various corporate reactants databases and inventory houses and return the hits seamlessly back into PGVL Hub design session. From user s point of view, the ChemSelect AQB component is just part of PGVL Hub. 

This structure browsing procedure has proved very popular with users at Pfizer, both as a simple alternative to substructure search, and as a means of identif5dng analogous structures (lateral thinking ). Examples of the sort of similar structures produced from browse searches are shown in Figures 1 and 2 (not ranked in order) other examples are given in reference 4. Some of these would clearly be retrieved by conventional substructure searches, while others would not. 

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