Databases of 2D Structures

The linking of fragment-based and MCS-based searching provides an extremely powerful mechanism for subsimilarity searching (and could clearly be extended to both similarity and supersimilarity searching) with developments in computing power, it is likely that such systems will become widely used over the next few years. 

There are at least three reasons why one might wish to apply cluster analysis to a large chemical database. Hie simplest approach is to cluster the output resulting from a substructure search that retrieves too many molecules, to enable the searcher to gain a rapid overview the extent of the structural heterogeneity in the retrieval list. Second, one may wish to duster an entire database so that individual dusters can be retrieved and examined by more computationally expensive procedures this can be particularly appropriate for structure—activity techniques that require homogeneous subsets of molecules from the main database. Finally, there has been substantial interest in the use of 

There are many different types of clustering methods,thejg have been several evaluations of these for use in a chemical context, as we now discuss. 

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Boulevard Vincent Auriol 75646 Paris Cedex 13, France Tel. 33-144-23-64-64, fax 33-144-23-64-65 Preparation and transfer of queries for DARC database searches. PCs. DARC Inhouse for maintaining databases of 2D structures on VAX. 

The popular program, CONCORD, of Pearlman [4,20] was for a long time the most widely used method for converting large databases of 2D structures to 3D representations. The program is based on rules and a simplified force field method. It performs the following steps for model building ... 

The last few years have seen substantial interest in the development of database-searching systems for files of 3D structures. The atom coordinate information in such databases is obtained either experimentally, usually from the Cambridge Structural Database, which contains X-ray structures that have been reported in the published literature,or by the use of a struaure-builder, which is a computer program that calculates an approximate 3D structure from a 2D connection table. - The best known of such programs is CONCORD, which uses a knowledge base of rules that describe preferred molecular conformational patterns and a simplified force-field. CONCORD has been widely used for the conversion of both in-house and public databases of 2D structures to 3D form. 

In the earlier section on the Chemical Abstracts Service (CAS), we gave a brief overview of the range of similarity measures that are under investigation by Fisanick et al. and described the novel descriptors that these workers have developed for similarity searching in databases of 2D structures. Their studies have also involved both geometric and property based 3D similarity measures in all, a molecule is characterized by a maximum of no fewer than 3172 different features. 

Figure 2.150. Ligprep is used for the rapid conversion of 2D structure files into accurate 3D models suitable for use in database screens and other applications. At the user s discretion Ligprep can generate multiple protonation states, enumerate chiralities, and generate tautomeric forms of the ligand...

Tel. 44-0625-871126, fax 44-0625-871128 Structure building, manipulation. Force field minimization. Stick, ball-and-stick, and space-filling display. Sabre for managing a database of 2D chemical structures. Macintosh. PC-Chemmod for structure building, manipulation, energy minimization of molecules with up to 2000 atoms. Stick and space-filling display. PCs. 

Management of databases of 2D chemical structures. PsiGen for 2D chemical structure drawing. PCs under Windows. 

Gesellschaft fiir Technisch-Wissenschaftliche Software mbH Rudolf Diesel Strasse 1 W-8032 Grafelfing, Germany Tel. 49-089-855056, fax 49-089-852170 Management of databases of 2D chemical structures. PC, IBM, and VAX. 

Tel. 800-232-2224, 203-335-0906, fax 203-336-2481 Display and manipulation of 3D models using keyboard input. Molecular Animator for creating and displaying 3D models. Molecular Graphics for display and manipulation of atomic coordinate data. ChemFile II for creating databases of 2D chemical structures with associated text. PCs and Macintosh. 

Drawing 2D chemical structures. ChemWhere for searching for MPG structures in word processing documents. Datalyst II for management of databases of chemical structure in dBASE-compatible files. ConSystant for reformatting data files between software applications. Chemeleon from Exographics for data file conversions. PCs. 

Tel. 415-903-3900, fax 415-961-0584, e-mail support(5)biocad.com Catalyst/Hypo for building molecular models, systematic conformational searching, and statistical fitting of 3D structural features to bioactivities. Phar-macophoric hypotheses can be used to search for matches in databases of 3D structures. Catalyst/Info for managing databases of ID, 2D, and 3D data. Silicon Graphics and networked Macintosh and PCs. 

There is a wealth of databases that code available compounds typically in the two-dimensional standard data (2D-SD) format including connectivity from MACCS (32, 64). The most common databases are the Available Chemicals Directory (ACD) (42), Spresi (65), Chemical Abstracts Database (66), and the National Cancer Institute Database (67, 68). Many vendors of chemicals also provide searchable databases with 2D-structure and... 

Structure building, manipulation. Van der Waals and elearostatic energy minimization by MM2 and MNDO. Stick and ball-and-stick display. Report generation, interface to ChemDraft for 2D chemical structure drawing. Database of optimized structures of 2000 compounds used in the development of the semi-empirical methods in MOPAC and AMPAC. PC. 

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