Chemical Substructure Search in SQL

publication · 10 years ago
by Adel Golovin, Kim Henrick (EMBL-EBI Hinston Hall Genome Campus)
We present a novel technique for a fast chemical substructure search on a relational database by use of a standard SQL query. The symmetry of a query graph is analyzed to give additional constraints. Our method is based on breadth-first search (BFS) algorithms implementation using Relational Database Management Systems (RDBMS). In addition to the chemical search we apply our technique to the field of intermolecular interactions which involves nonplanar graphs and describe how to achieve linear time performance along with the suggestion on how to sufficiently reduce the linear coefficient. From the algorithms theory perspective these results mean that subgraph isomorphism is a polynomial time problem, hence equal problems have the same complexity. The application to subgraph isomorphism in chemical search is available at and The application to the network of molecule interactions is available at
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