Chemical structure databases

The first task was the aeation of large 3D chemical structure databases. By devising so-called fast Automatic 3D model builder, software such as the CORINA [27, 28] and CONCORD [29, 30] programs resulted in a boom in 3D database development (see Section 2.9 in this book and Chapter II, Section 7.1 in the Handbook). A subsequent step was the development of fast... 

Downs G M, P Willett and W Fisanick 1994. Similarity Searching and Qustering of Chemical Structure Databases using Molecular Property Data, journal of Chemical Information and Computer Sciences 34 1094-1102. 

P Willett. Algorithms for the calculation of similarity m chemical structure databases. In MA Johnson, GM Maggiora, eds. Concepts and Applications of Molecular Similarity. New York Wiley, 1990, pp 43-63. 

CHEMOINFORMATICS TECHNIQUES FOR PROCESSING CHEMICAL STRUCTURE DATABASES... 

Downs GM, Willett P. Clustering of chemical structure databases for compound selection. In van de Waterbeemd H, editor, Advanced computer-assisted techniques in drug discovery. Weinheim VCH Verlag, 1994. p. 111-30. 

The distribution of Tanimoto indices for randomly selected (or all) pairs of structures characterizes the diversity of a chemical structure database (Demuth et al. 2004 Scsibrany et al. 2003). For structure similarity searches, a number of other similarity measures have been suggested (Gasteiger and Engel 2003 Willett 1987). 

Today, pharmaceutical companies are linking CDS to business systems such as SAP, chemical structure databases, electronic laboratory notebooks, and corporate data warehousing solutions. Many commonly used software products utilize COM Automation (Microsoft s Component Object Model) to provide a powerful array of programmable objects that allow seamless connections between applications. 

POETTER, T. and Matter, H. Design and evaluation of optimally diverse compound subsets from chemical structure databases. Book of Abstracts, 213th ACS National Meeting. San Francisco, 1997, 1431-1436. 

Raymond, J. W. and Willett, P. (2002) Effectiveness of graph-based and fingerprint-based similarity measures for virtual screening of 2D chemical structure databases. 

Voigt, J. H., Bienfait, B., Wang, S., and Nicklaus, M. C. (2001) Comparison of the NCI open database with seven large chemical structural databases. J. Chem. Inf. Comput. Sci. 41, 702-712. 

Potter, T., Matter, H. (1998) Random or rational design Evaluation of diverse compound subsets from chemical structure databases. J Med Chem 41, 478M88. 

Besides chemical structure databases, both proprietary and public databases contain a wealth of numerical and textual information pertinent to chemistry. 

It is therefore important to know how to access and trawl thorough this internal knowledge so that you can add value to the company, e.g. Chemical structural databases, project data, information from theoretical modelling. 

Stanley V. Kasparek, Computer Graphics and Chemical Structures Database Management Systems, CAS Registry, Chembase, REACCS, MACCS-II, Chemtalk, Wiley, New York, 1990. 

The chemical structure database and registration procedure play dual roles in an enterprise screening informatics environment. These components are essential to the transactional HTS informatics system and serve as the basis for cheminformatics data analysis. While capturing the chemical structures for association with the final screening endpoints, this system also captures and applies the organizational chemical business rules to validate and standardize chemical structures and canonicalize their representations. Structural representation is a critical prerequisite for any subsequent cheminformatics analysis. 

Nowadays, thanks to the availability, cost, and ease-of use of chemical structure databases, many of these text databases have been converted into a structure format, and most chemical databases are now structure searchable. A simple search of the Internet will show that many databases still lack chemical structures and therefore are not searchable by structure in the original format, for example, an online HTML page. These pages, however, can contain valuable information and, with the application of the appropriate name-to-structure (N2S) conversion tools can be made searchable. 

Clearly, there is a pressing need for an equivalent to optical character recognition, optical chemical structure recognition, that can automatically turn bitmapped structural diagrams into structure descriptions—connection tables or equivalent structural strings—that are suitable for input into chemical structure databases. 

Structure building, manipulation. Van der Waals and electrostatic energy minimization by MM2 and MNDO. Stick or ball-and-stick display. Report generation, interface to ChemDraft for drawing chemical structures. Database of structures of compounds used in the development of the semiempirical methods in MOPAC and AMPAC. PC. 

Downs, G.M., Willett, P. and Fisanick W. Similarity Searching and Clustering of Chemical-Structure Databases Using Molecular Property Data. J. Chem. Inf. Comput. 

Potter, T. Matter, H. Random or Rational Design Evaluation of Diverse Compound Subsets from Chemical Structure Databases. J. Med. Chem., 1998, 41, 478-488. 

Chemical structure database, structure viewing support by Chemscape Chime U.S. National Library of Medicine, National Institute of Health http //sis.nlm.nih.gov/Chem/ ChemMain.html... 

H. van de Waterbeemd, Ed., VCH Publishers, Weinheim, 1994, pp. 111—130. Clustering of Chemical Structure Databases for Compound Selection. 

Similarity Searching and Clustering of Chemical-Structure Databases Using Molecular Property Data. 

Deduplication. When registering into a chemical structure database, the process of finding whether the given structure already exists in the database. This usually involves performing an exact match search with the given structure as the search query. Note that the definition of exact match may vary with the database, and it may even be configurable. For example, some databases may consider tautomers to be acceptable as exact matches, whereas others may require a more strict definition. 

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