Topological query features

Fuzzy 2D substructure searching is an extension of substructure searching to the minor extent that it permits the expansion of the query formulation vocabulary to include topological features and substructural wildcards described above. This involves the retrieval of all entities in a CIR system that contain the user-defined partial structure and that satisfy whatever wildcard specification pattern has been specified. The query identifies the partial structure and simple wildcard substitution patterns exactly. As with substructure searching, the use of query features on a partial structure will always identify structures which are equal in size or larger than the query. 

Yak/Prgen and COMPASS work fundamentally with the surface of molecules, and derive representations of the predicted binding surface of the receptor ( pseudoreceptor ). APOLLO appears to work with features —groups on the molecule that meet specific topological criteria (i.e., which match a specified subgraph isomorphism query) these features must be defined by the user. 

Use more specific queries with wider ranges of values for 3D features to generate a large initial list rapidly. More specific search queries can be created by including as much topology as possible. 

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