ChemDB

Many commercial vendors and academic labs provide collection of compounds or fragments (Sigma-Aldrige, Available Chemicals Directory (ACD) (http //www.symyx.com), Maybridge (www.maybridge.com), TCI America (http //www. tciamerica.com), ChemDB (51) (http //cdb.ics.uci.edu), ZINC... 

Chen, J., Swamidass, S. J., Dou, Y., Bruand, J., Baldi, P. (2005) ChemDB a public database of small molecules and related chemoinformatics resources. Bioinformatics 21,4133 139. 

ICM and DOCK 1 were used to virtually screen the University of California, Irvine, ChemDB database and NCI databases to identify AccD5 inhibitors... 

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). 

Tel. 800-753-4227, 614-447-3600, fax 614-447-3713 (U.S.A.), tel. 49-7247-808555, fax 49-7247-808666 (Germany), tel. 81-3-3581-6448, fax 81-3-3581-6446 (Japan), e-mail kpc23 cas.org Subsets of structures from the Chemical Abstracts Service registry file three-dimensionalized with CONCORD. Searchable by SYBYL/3DB, MACCS-3D, ChemDBS-3D, and CAVEAT. 

Chen, J.H., Linstead, E., Swamidass, S.J., Wang, D., and Baldi, P. (2007) ChemDB update flill-text search and virtual chemical space. Bioinformatics, 23, 2348-2351. 

Tel. 614-447-3600, fax 614-447-3713, e-mail kpc23 cas.org Subsets of structures from the Chemical Abstracts registry file three-dimensionalized with CONCORD. Searchable by SYBYL/3DB, MACCS-3D, ChemDBS-3D, and CAVEAT. 

Ricketts, E.M. Rradshaw, J. Hann, M. Hayes, F. Tanna, N. Ricketts. D.M. Comparison of conformations of small-molecule structures from the Protein Data-Bank with those generated by concord, cobra, chemdbs-3D, and converter and those extracted from the Cambridge Structural Database. J. Chem. Inf. Comput. Sci. 1993, 33. 905-925. 

Some databases, such as WebReactions (http //www.webreactions.net/), REACCS (http //www.mdl.com/company/about/history.jsp) or MOS (http // www.accelrys.com/products/datasheets/chemdb mos a4.pdf) are organized in a similar fashion and allow one to search for real reactions that correspond to certain half-reactions. 

Syntax Select from ChemDB.Molecules where Name like %cyclohexane% Output of Query ... 

Example for Alter Table ChemDB.Molecules for change field name Name to CompoundName. ... 

Syntax ALTER TABLE ChemDB.Molecules CHANGE Name Compound-... 

A web-based predictor, AquaSol, is available online through the ChemDB portal that can be applied to the problem of predicting aqueous solubility [54]. Molpro, another module in the portal, predicts molecular properties other than 3D stmctures. 

The free online database ChemDB [cdb.ics.uci.edu and J. Chen et al.. Bioinformatics, 21, 4133 (2005) 23, 2348 (2007)] contains about 5 million commercially available compounds whose three-dimensional structures have been estimated using CORINA the database can be efficiently searched for desired structural features. After entering the name or SMILES string of what you are looking for, the search may give you more than one result. Choose the molecule you want by clicking on the number near its formula. You will get a rotatable three-dimensional model. In the drop-down list, choose the XYZ - Xmol XYZ format and click on Download Chemical. Save it to your computer. When you open the saved file with a word processor, you will see the Cartesian coordinates. 

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