Stereochemistry retrieval

With its flexible and logical search language, REACCS can retrieve molecular stmctures, the atoms and bonds that are transformed ia a reaction, relative and absolute stereochemistry, the role (reactant, product, solvent, or catalyst) of a molecule ia a reaction, reaction data (eg, temperature and yield), hterature references, and keyword descriptions of reaction types. 

Fig. 5. (a and b) Two perpendicular orientations of direct carboxylate-zinc interactions retrieved from four metalloprotein structures contained in the Brookhaven Protein Data Bank. Orientation (a) represents the carboxylate group as found in Fig. 3. The coordination stereochemistry is syn for each example.

The Protein Data Bank (PDB http //www.pdb.org) is the worldwide repository of three-dimensional structural data of biological macromolecules, such as proteins and nucleic acids (Berman et al. 2003). The Protein Data Bank uses several text file-based formats for data deposition, processing, and archiving. The oldest of these is the Protein Data Bank format (Bernstein 1977), which is used both for deposition and for retrieval of results. It is a plain-text format whose main part, a so-called primary structure section, contains the atomic coordinates within the sequence of residues (e.g., nucleotides or amino acids) in each chain of the macromolecule. Embedded in these records are chain identifiers and sequence numbers that allow other records to reference parts of the sequence. Apart from structural data, the PDB format also allows for storing of various metadata such as bibliographic data, experimental conditions, additional stereochemistry information, and so on. However, the amount of metadata types available is rather limited owing to the age of the PDB format and to its relatively strict syntax rules. 

Flexmatch Search. Term used in MDL structure searching to allow "relaxed" exact match searching of structures. One can specify, for instance, that everything must match except bond orders, or stereochemistry, or valence at atom centers, etc. By turning on or off various flags, one can for a given structure query, retrieve isomers of various types, salts of a the structure, or instances of the structure that may contain different values of certain types of attached data. 

V. Prelog, who shared the 1975 Nobel prize in chemistry for his work in stereochemistry, has pointed out that stereochemistry is not a branch of chemistry but a point of view. Most molecules are non-planar. Whether one in fact looks at them in 3-D depends on one s needs and one s knowledge and background. In the sequel, I shall explore the three-dimensional point of view in stereochemical history, in stereochemical concepts and finally in information storage and retrieval. 

Figure la shows an example of a stereochemical comparison involving absolute and relative stereochemistry. The query substructure and the structure, which is presumed to have been retrieved by a topological search, each have four stereocentres. It is assumed that in the query these stereocentres are grouped into... 

Stereochemical representation has been an integral part of the CAS Chemical Registry System since its inception in 1965 (see Stereochemistry Representation and Manipulation). Stereoisomers are considered to be different, individual substances, and each is assigned its own CAS Registry Number. The unique identification of stereoisomers permits the storage and retrieval of information collected from scientific literature about a specific isomer. About one-fourth of the over 17 million substances in the Registry File contain stereo information. 

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