Database Indexing for a faster Substructure Search

In our first release of MMsINC (see recent post) we developed a strategy that can help in making faster a substructure search in huge databases.

Rules:
1) choose a fragmentation algorithm
2) fragment all the compounds in your database
3) store the fragments in your database

Then, when the user submits a query, you can apply your fragmentation tool to the query compoud.
If you are lucky, you can restrict the search space to the database compounds that share the same fragments of the query.
You can then apply the exact substructure search to this reduced set of compounds.

You need more disk space, but in this way you can save computation time.

MMsINC

What is MMsINC?

MMsINC is a database of non-redundant, richly annotated, and biomedically relevant chemical structures.

A primary goal of MMsINC is to guarantee the highest quality and the uniqueness of each entry. MMsINC then adds value to these entries by including the analysis of crucial chemical properties such as ionization and tautomerization processes, and the in silico prediction of 24 important molecular properties in the biochemical profile of each structure. MMsINC is consequently a natural input for different chemoinformatics and virtual screening applications. In addition, MMsINC supports various types of queries, including substructure queries and the novel "molecular scissoring" query.

MMsINC is interfaced with other primary data collectors such as PubChem, Protein Data Bank (PDB), the Food and Drug Administration (FDA) database of approved drugs, and ZINC.

The current database contains about 4 million unique compounds. For all the molecules, we calculate 24 molecular properties useful for quantitative structure-activity relationship (QSAR), diversity analysis or combinatorial library design.