Representation of chemical information in OASIS centralized 3D database for existing chemicals.
The present inventory of existing chemicals in regulatory agencies in North America and Europe, encompassing the chemicals of the European Chemicals Bureau (EINECS, with 61 573 discrete chemicals); the Danish EPA (159 448 chemicals); the U.S. EPA (TSCA, 56 882 chemicals; HPVC, 10 546 chemicals) and pesticides' active and inactive ingredients of the U.S. EPA (1379 chemicals); the Organization for Economic Cooperation and Development (HPVC, 4750 chemicals); Environment Canada (DSL, 10851 chemicals); and the Japanese Ministry of Economy, Trade, and Industry (16811), was combined in a centralized 3D database for existing chemicals. The total number of unique chemicals from all of these databases exceeded 185 500. Defined and undefined chemical mixtures and polymers are handled, along with discrete (hydrolyzing and nonhydrolyzing) chemicals. The database manager provides the storage and retrieval of chemical structures with 2D and 3D data, accounting for molecular flexibility by using representative sets of conformers for each chemical. The electronic and geometric structures of all conformers are quantum-chemically optimized and evaluated. Hence, the database contains over 3.7 million 3D records with hundreds of millions of descriptor data items at the levels of structures, conformers, or atoms. The platform contains a highly developed search subsystem--a search is possible on Chemical Abstracts Service numbers; names; 2D and 3D fragment searches; structural, conformational, or atomic properties; affiliation in other chemical databases; structure similarity; logical combinations; saved queries; and search result exports. Models (collections of logically related descriptors) are supported, including information on a model's author, date, bioassay, organs/tissues, conditions, administration, and so forth. Fragments can be interactively constructed using a visual structure editor. A configurable database browser is designed for the inspection and editing of all types of data items. Database statistics are maintained on the number and quality of structures, conformers, and descriptors. Reports can be generated presenting any chosen subset of structures and descriptors into different formats suitable for inclusion into documents. In addition to fixed report formats, there is a powerful report template designer module with a visual report template editor to produce a customized page layout. The database is compatible at the import/export level with SDF, MOL, SMILES, and other known formats. The precalculated centralized 3D database could be useful for quantitative structure-activity relationship developers avoiding the time-consuming and cumbersome 3D calculation phase of model development.
Nikolov
Nikolai
N
Centre of Biomedical Engineering Ivan Daskalov-Bulgarian Academy of Sciences, Bl. 105 Acad. G. Bonchev Str., 1113 Sofia, Bulgaria.
Grancharov
Vanio
V
Stoyanova
Galya
G
Pavlov
Todor
T
Mekenyan
Ovanes
O
D000465:Algorithms; D000818:Animals; D002621:Chemistry / Q000379:methods*; D003198:Computer Simulation; D016208:Databases, Factual; D004353:Drug Evaluation, Preclinical / Q000379:methods*; D004784:Environmental Monitoring / Q000379:methods; D021621:Imaging, Three-Dimensional; D008956:Models, Chemical; D015233:Models, Statistical; D015394:Molecular Structure; D011108:Polymers / Q000737:chemistry; D051381:Rats; D014481:United States; D014484:United States Environmental Protection Agency
D011108:Polymers