Searching molecular databases

Other programs are designed to dock ligands in a 3D receptor, as well as to determine the shape of the receptor. If the shape of the cavity is known, then this information can be used to search molecular databases for small compounds that will be complementary. Indeed, it is fairly easy to find weakly active ligands in this manner. 

Altschul S F, M S Boguski, W Gish and J C Wootton 1994. Issues in Searching Molecular Sequen Databases. Nature Genetics 6 119-129. 

There are now extensive databases of molecular structures and properties. There are some research efforts, such as drug design, in which it is desirable to hnd all molecules that are very similai to a molecule which has the desired property. Thus, there are now techniques for searching large databases of structures to hnd compounds with the highest molecular similarity. This results in hnding a collection of known structures that are most similar to a specihc compound. 

Another technique employs a database search. The calculation starts with a molecular structure and searches a database of known spectra to find those with the most similar molecular structure. The known spectra are then used to derive parameters for inclusion in a group additivity calculation. This can be a fairly sophisticated technique incorporating weight factors to account for how closely the known molecule conforms to typical values for the component functional groups. The use of a large database of compounds can make this a very accurate technique. It also ensures that liquid, rather than gas-phase, spectra are being predicted. 

Nuclear Magnetic Resonance Spectroscopy. Bmker s database, designed for use with its spectrophotometers, contains 20,000 C-nmr and H-nmr, as weU as a combined nmr-ms database (66). Sadder Laboratories markets a PC-based system that can search its coUection of 30,000 C-nmr spectra by substmcture as weU as by peak assignments and by fiiU spectmm (64). Other databases include one by Varian and a CD-ROM system containing polymer spectra produced by Tsukuba University, Japan. CSEARCH, a system developed at the University of Vieima by Robien, searches a database of almost 16,000 C-nmr. Molecular Design Limited (MDL) has adapted the Robien database to be searched in the MACCS and ISIS graphical display and search environment (63). Projects are under way to link the MDL system with the Sadder Hbrary and its unique search capabiHties. 

SF Altschul, MS Boguski, W Gish, JC Wootton. Issues in searching molecular sequence databases. Nature Genet 6 119-129, 1994. 

In analyses where molecular masses are being matched, more accurate mass measurements provide more reliable matches and identifications.26,65,66 In a reference laboratory the mass accuracy to several decimal points, provided by a Fourier transform ion cyclotron resonance mass analyzer, may be desirable. In field or portable systems there is usually a trade-off in mass accuracy for size and ruggedness. Reliable identifications can be made with moderate mass accuracy, even 1 Da, if a large enough suite of molecular ions is recorded and used to search the database. If both positive ion and negative ion spectra are... 

Johnson R.S. and Taylor J.A. (2000), Searching sequence databases via de novo peptide sequencing by tandem mass spectrometry, in Methods in Molecular Biology, Vol. 146, Mass Spectrometry of Proteins and Peptides, pp. 41-61, Chapman J.R., Ed., Humana Press, Totowa, NJ. 

Searching through Databases Applications of network BLAST server, 266, 131 Entrez molecular biology database and retrieval system, 266, 141 applying motif and profile searches,... 

MAECIS contains five major sections that are integrated into a single system. At its center is a database management system that handles the storage and updating of data and chemical structures. Associated with this section is an information retrieval section that allows one to search the database for specific information composed of any combination of data and/or substructures. Once information is retrieved, it can be displayed on a computer terminal or sent to a printer for hardcopy output using the display section of MAECIS which includes the ability to display chemical structures in various formats. The final two sections of MAECIS allow for the manipulation of chemical structures and the calculation of various molecular properties that are related to chemical structures. 

Molecular databases and the associated data banks require the development of a conceptual structure for the information stored about the molecules, descriptive language representing the data, and methods for analysis enabling molecular modeling, similarity searches, classification, visualization, or other uses of the database.320 Currendy, the Protein Data Bank (PDB http 7www.rcsb.org/pdb/) is one of the best known examples of a molecular database. The PDB is a worldwide archive of three-dimensional structural data of biological macromolecules.321 The PDB is a common accentor to many structural databases.322 The success of... 

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