Search database

Usually an Internet user learns after a while where to go for specific information The Browser provides a bookmark tlmction where all these addresses can be organized by different subjects Typical bookmark folders are Societies, Companies, Journals, Institutes, Databases, Search engines The NDTnet Journal provides a virtual library that makes it easy for newcomers to find NDT sites. Unfortunately, some sites provide a lot of information but do not offer a search function. 

Most database users do not know how the data are organized in a database system (DBS) they depend solely on the application programs. This is sufficient for most database searches where users can receive large amounts of results quickly and easily, e.g., on literature or other information. Nevertheless, a basic knowledge on where and how to find deeper or more detailed information is quite useful. Due to their complex nature, comprehensive searches (e.g., for processes or patents) are not recommended for beginners. However, most local (in-house), online, and CD-ROM databases provide extensive tutorials and help functions that are specific to the database, and that give a substantial introduction into database searching. 

In order to perform a database search the structural key of the query molecule or substructure is compared with the stored structural keys of the database entries. This implies that each array element in the structural key has to be defined initi-... 

Following the similar structure - similar property principle", high-ranked structures in a similarity search are likely to have similar physicochemical and biological properties to those of the target structure. Accordingly, similarity searches play a pivotal role in database searches related to drug design. Some frequently used distance and similarity measures are illustrated in Section 8.2.1. 

A useful empirical method for the prediction of chemical shifts and coupling constants relies on the information contained in databases of structures with the corresponding NMR data. Large databases with hundred-thousands of chemical shifts are commercially available and are linked to predictive systems, which basically rely on database searching [35], Protons are internally represented by their structural environments, usually their HOSE codes [9]. When a query structure is submitted, a search is performed to find the protons belonging to similar (overlapping) substructures. These are the protons with the same HOSE codes as the protons in the query molecule. The prediction of the chemical shift is calculated as the average chemical shift of the retrieved protons. 

NMR spectra have been predicted using quantum chemistry calculations, database searches, additive methods, regressions, and neural networks. 

Correlations between structure and mass spectra were established on the basis of multivariate analysis of the spectra, database searching, or the development of knowledge-based systems, some including explicit management of chemical reactions. 

It is also possible to extend this concept to cover the presence of more than one distinct segm pair in a pair of sequences (for example, if there are three MSPs present with scores of 40, and 50 then one can calculate the probabOity of finding three pairs with at least a score of by chance). The ability of BLAST to provide a quantitative significance of any match fou is a particularly useful feature of the program, which, with its continuing development a availability, has made it the most widely used method for sequence database searching. 

Altschul S F, T L Madden, A A Schaffer, J Zhang, Z Zhang, W Miller and D J Lipman 1997. Gapped BLAST and PSI-BLAST A New Generation of Protein Database Search Programs. Nucleic Acids Research 25 3389-3402. 

D database searching. As each conformation is generated an appropriate bit is set in the binary key. At me, the binary key appropriate to the pharmacophore is set up and compared with the keys in the database. 

A flow chart showing the various phases leading to the final compound is reproduced ii Figure 12.35. The first step was a 3D database search of a subset of the Cambridge Structura Database. The pharmacophore for this search comprised two hydrophobic groups and i... 

Good A C and J S Mason 1995. Three-Dimensional Structure Database Searches. In Lipkowitz K B and D B Boyd (Editors) Reviews in Computational Chemistry Volume 7. New York, VCH Publishers, pp. 67-117. 

H-J 1998. Prediction of Binding Constants of Protein Ligands A Fast Method for the aritisation of Hits Obtained from De Novo Design or 3D Database Search Programs. Journal of nputer-Aided Molecular Design 12 309-323. 

The generation of loops is necessary because disconnected regions are often separated by a section where a few amino acids have been inserted or omitted. These are often extra loops that can be determined by several methods. One method is to perform a database search to find a similar loop and then use its geometric structure. Often, other conformation search methods are used. Manual structure building may be necessary in order to find a conformation that connects the segments. Visual inspection of the result is recommended in any case. 

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. 

Database searches can be used to find a reference to a known compound with a matching substructure. This is a particularly good technique if a portion of the molecule has an unusual structure. It may indicate a synthesis route or simply identify a likely starting material. 

The molecular overlay experiment orients the molecules to hnd the best RMS or held ht. The held ht is based on electrostatic and steric interactions. The application can hnd either the best total alignment of all molecules or the best match of all molecules to a specihed target molecule. Alignment can include a database search for conformers that show the best alignment based on the molecules under study. 

NERAC, bibhography. Full Text Database Searching, pub. no. PB92-860469, ToUand, Conn., 1992. 

Sample and status tracking Database searches Numbers of samples assayed Tests utilised... 

Secondary sources of patent information, Advances in patent documentation. Types of patent information searches. On-line database searching methods. Cross-file and multifile techniques. 

Many other compounds are presendy in use a 1993 database search showed 27 active ingredients in 212 products registered by the U.S. EPA for human use as repellents or feeding depressants, including octyl bicycloheptene dicarboxamide (A/-2-ethylhexylbicyclo[2.2.1]-5-hepten-2,3-dicarboxamide), dipropyl isocinchomeronate (2,5-pyridine dicarboxyhc acid, dipropyl ester), dimethyl phthalate, oil of citroneUa, cedarwood oil, pyrethrins, and pine tar oil (2). Repellent—toxicant or biting depressant systems are available which are reasonably comfortable for the user and can protect completely against a number of pests for an extended period of time (2). 

Chemically related database searches can be used to estabhsh concepts and patentable ideas. For instance, searches have identified researchers using particular monomers in a potentially patentable latex formulation found precedents for a polymeric emulsifier summarized pubHcations of people being considered as consultants, expert witnesses, employees or speakers to an industrial group and provided market description information for a new pigment manufacturing firm to identify target markets. 

Fig. 2. Growth in number of online database searches on principal U.S. vendors of word-oriented databases.

Whereas Figure 1 represents worldwide data for all types of pubHcly available databases. Figure 2, showing growth in database searches, represents only a portion of those databases, ie, U.S. usage of word-oriented databases in the information center/Hbrary market. 

Many databases can be classified in multiple ways because of multiple type data, eg, text and numeric data, text and image data, image and audio data, etc. Also included in the data presented in Table 1 are two additional classes of databases, electronic services and software. Both of these data types could also be classed by form of representation because of use of words and numbers. However, the way in which these databases are used is different and they have special characteristics. Thus they are presented as additional classes. Whereas electronic information services such as bulletin boards, electronic mail, and electronic conferencing contain data that are transitory and nonarchival, these must be included among databases because several of the principal vendors seU these services in the same way as database search services are sold. 

Producers. The producers of databases are sometimes called database publishers because they make pubHc their databases. Some producers pubhsh hardcopy counterparts to databases and so are pubHshers in the traditional sense others pubHsh data only in electronic form. Database producers are responsible both for the deterrnination of content and for database production. Most producers offer their databases for lease or Hcense to private organisations or database vendors. Vendors offer database search services to the marketplace on a fee basis. An increasing number of producer/vendors such as Mead Data Central, U.S. National Library of Medicine, and DRI/McGraw-HiU. (formerly Data Resources), offer search services (batch or online) from their own databases as well as from the databases of other products. 

There are two main classes of loop modeling methods (1) the database search approaches, where a segment that fits on the anchor core regions is found in a database of all known protein structures [62,94], and (2) the conformational search approaches [95-97]. There are also methods that combine these two approaches [92,98,99]. 

To overcome the limitations of the database search methods, conformational search methods were developed [95,96,109]. There are many such methods, exploiting different protein representations, objective function tenns, and optimization or enumeration algorithms. The search algorithms include the minimum perturbation method [97], molecular dynamics simulations [92,110,111], genetic algorithms [112], Monte Carlo and simulated annealing [113,114], multiple copy simultaneous search [115-117], self-consistent field optimization [118], and an enumeration based on the graph theory [119]. 

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