Databases Structural Database

HIV Protease Database Structure database of HIV proteases complexed with their inhibitors http 1/srdata.nist.gov/hivdb/... 

Chemical Abstracts Service Information System Chemical Engineering Databases Chemical Safety Information Databases Factual Information Databases Inorganic Chemistry Databases Internet Internet-based Computational Chemistry Tools Online Databases in Chemistry Reaction Databases Structure Databases. 

Inorganic Chemistry Databases Inorganic Three-dimensional Structure Databases Structure Databases Structure Representation. 

Chemical Abstracts Service Information System Computer Graphics and Molecular Modeling Electronic Publishing of Scientific Manuscripts Factual Information Databases Internet-based Computational Chemistry Tools Molecular Models Visualization Nucleic Acids Qualitative Modeling Online Databases in Chemistry Protein Data Bank (PDB) A Database of 3D Structural Information of Biological Macromolecules Reaction Databases Spectroscopic Databases Structure Databases. 

As source of infonnation we use the Surface Structure Database [14], a critical compilation of surface structures solved in detail, covering the period to the end of 1997. It contains 1113 structural detenninations with, on average, two detenninations for each stmcture thus there are approximately 550 distinct solved stnictures available. 

Watson P R, Van Hove M A and Hermann K 1999 NIST Surface Structure Database Ver. 3.0 (Gaithersburg, MD NIST Standard Reference Data Program)... 

The JME Editor is a Java program which allows one to draw, edit, and display molecules and reactions directly within a web page and may also be used as an application in a stand-alone mode. The editor was originally developed for use in an in-house web-based chemoinformatics system but because of many requests it was released to the public. The JME currently is probably the most popular molecule entry system written in Java. Internet sites that use the JME applet include several structure databases, property prediction services, various chemoinformatics tools (such as for generation of 3D structures or molecular orbital visualization), and interactive sites focused on chemistry education [209]. 

The JME can also serve as a query input tool for structure databases by allowing creation of complex substructure queries (Figure 2-130), which are automatically translated into SMARTS [22]. With the help of simple HTML-format elements the creation of 3D structure queries is also possible, as were used in the 3D pharmacophore searches in the NCI database system [129]. Creation of reac-... 

Typical numeric databases are Beilstein, Speclnfo, DETHERM, and the Cambridge Structural Database. 

Structure databases are databases that contain information on chemical structures and compounds. The compounds or structure diagrams are not stored as graphics but are represented as connection tables (see Section 2.4). The information about the structure includes the topological arrangement of atoms and the connection between these atoms. This strategy of storage is different from text files and allows one to search chemical structures in several ways. 

Examples of structure databases are Beilstein, Gmehn, and CAS Registry. 

Figure 5-18. Interactive display of the detailed Beilstein database structure.

After return to the Commander window, the reaction retrieval may be executed separately 629 Dicls-Aldcr reactions between aliphatic dienes and cyclic dicno-pliiles are found. This partial result can be narrowed down by restricting tlie reaction conditions by means of the fact editor, The search field codes for the yield and the temperature can be found to be RX.NYD and RX.T, respectively, either by browsing the database structure or by applying the Find option, as described in the first example. To ensure that the retrieved reaction conditions belong to the same experiment, both search terms must be connected by means of the PROXIMITY operator. Before the retrieval is started, the option "Refine results in... 

The two major databases containing information obtained from X-ray structure analysis of small molecules are the Cambridge Structural Database (CSD) [25] and the Inorganic Crystal Structure Database (ICSD) [26] both are available as in-house versions. CSD provides access to organic and organometallic structures (mainly X-ray structures, with some structures from neutron diffraction), data which are mostly unpublished. The ICSD contains inorganic structures. 

The Cambridge Structural Database (CSD) contains crystal structure information... 

Compounds are stored in reaction databases as connection tables (CT) in the same manner as in structure databases (see Section 5.11). Additionally, each compound is assigned information on the reaction center and the role of each compound in the specific reaction scheme (educt, product, etc.) (see Chapter 3). In addition to reaction data, the reaction database also includes bibliographic and factual information (solvent, yield, etc.). All these different data types render the integrated databases quite complex. The retrieval software must be able to recall all these different types of information. 

They are classified as bibliographic, factual, and structure databases. 

The Cambridge Structural Database (C5D) and the Inorganic Crystal Structure Database (ICSD) contain information obtained from X-ray structure analysis. 

The connection table of the query object (similarity probe) is processed to obtain the set of atom pairs, and then the database file is scanned to evaluate the similarity between the query and each of the database structures. The maximum number of structures that the program will select is specified, as well as the minimum similarity score that a database compoimd must show to be selected. Within these limits, the program will select from the database the structures that are most similar (with the highest similarity value) to the query and will create an output file of compoimd numbers and similarity values, sorted by decreasing similarity, for the selected compounds. 

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... 

The abbreviation QSAR stands for quantitative structure-activity relationships. QSPR means quantitative structure-property relationships. As the properties of an organic compound usually cannot be predicted directly from its molecular structure, an indirect approach Is used to overcome this problem. In the first step numerical descriptors encoding information about the molecular structure are calculated for a set of compounds. Secondly, statistical methods and artificial neural network models are used to predict the property or activity of interest, based on these descriptors or a suitable subset. A typical QSAR/QSPR study comprises the following steps structure entry or start from an existing structure database), descriptor calculation, descriptor selection, model building, model validation. 

The structure database has been enriched with the 3D structures of all compounds as generated by the 3D structure generator CORINA (sec Section 2.9,... 

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