Structure searching building databases

ChemCore module to three-dimensionalize 2D structures, interfaces to reformat MACCS, SMILES, or DARC-2D databases, ChemDBS-1 module to build 3D databases, and ChemDBS-3D module to search 3D databases. Database searching accounts for conformational flexibility while storing only one conformation. Chapman 8c Hall s 3D Dictionary of Drugs (12,000 medicinally interesting compounds), 3D Dictionary of Natural Products (50,000 antibiotics, alkaloids, and terpenoids), and 3D Dictionary of Fine Chemicals (105,000 organics). 

The following sections deal with structure searches in the Registry File. The commands are the same as for other structure databases. Particularities can be retrieved from the manual Building and Searching Structures on STN. 

The generation of loops is necessary because disconnected regions are often separated by a section where a few amino acids have been inserted or omitted. These are often extra loops that can be determined by several methods. One method is to perform a database search to find a similar loop and then use its geometric structure. Often, other conformation search methods are used. Manual structure building may be necessary in order to find a conformation that connects the segments. Visual inspection of the result is recommended in any case. 

The need for an overall and combined chemical structure and data search system became clear to us some time ago, and resulted in the decision to build CHIRBASE, a molecular-oriented factual database. The concept utilized in this database approach is related to the importance of molecular interactions in chiral recognition mechanisms. Solely a chemical information system permits the recognition of the molecular key fingerprints given by the new compound among thousands of fingerprints of known compounds available in a database. 

The capabilities of Leatherface are best illustrated with examples. While a number of these will be typical of substructural modifications involved in building virtual screening databases, we will also show how a 2-D structure editor can be used to establish relationships between molecules and perform unorthodox substructural searches. 

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