Database searching system

General NCBI Entrez http //www.ncbi.nlm.nih.gov/ http //www.ncbi.nlm.nih.gov/Entrez/index.html Bioinformatics databases and tools. A cross-database searching system. 

Registry Number. A unique identifier assigned to a chemical structure or other piece of data when it is registered into a database. The registry number may be internal, primarily for use by the database search system, or external, to be used by chemists and to link the data to other databases and files. 

Improtantly, there are several highly specific and useful database searching techniques have been duly introdueed into a plethora of most recent database searching system, namely ... 

UNITY-3DB The Tripos Associates Inc., USA provided also a database searching system that would enable the medicinal chemist to have an easy access to the utility in designing novel compounds based upon the versatality of enormous available and considerable functional characteristic features of such entities. 

Three different mass spectrometry search algorithms dominate the database searching systems commercially available today. The Cornell University Probability Based Matching (PBM) software, The Integrated Control System (INCOS) and the MassLib system (see below) with the SISCOM search software. 

The full GC/MS trace is analysed to locate the various components and candidate unknown spectra generated for searching in the reference databases using SIS-COM. The mass spectram database search system which comes with the MassLib package detailed below is called SISCOM (Search for Identical and Similar COM-ponents) [21]. The Identity search option looks for the unknown in the reference libraries and can handle binary mixtures as unknowns provided both substances are represented in the reference database. The identity search swaps to the similarity search mode if no identical hits have been found in the reference databases where characteristic ions in the unknown are searched in the reference libraries. 

A sequence tag from an unknown protein allows a number of further options for characterisation. Even a short stretch of amino acid sequence provides a powerful means of interrogating a protein database, and may provide a useful alternative to PMF in poor quality samples that may have peptides derived from more than one protein. More advanced database searching systems will find proteins with homologous sequences to that of the peptide tag. A good example of this type of database searching system is BLAST (Basic Local Alignment Sequence Tool), (Altschul et al., 1997). A modified form of this (MS BLAST) was used in conjunction with PMF to characterise the proteome of the yeast Pichia pastoris, whose genome has not been fully sequenced... 

The last few years have seen substantial interest in the development of database-searching systems for files of 3D structures. The atom coordinate information in such databases is obtained either experimentally, usually from the Cambridge Structural Database, which contains X-ray structures that have been reported in the published literature,or by the use of a struaure-builder, which is a computer program that calculates an approximate 3D structure from a 2D connection table. - The best known of such programs is CONCORD, which uses a knowledge base of rules that describe preferred molecular conformational patterns and a simplified force-field. CONCORD has been widely used for the conversion of both in-house and public databases of 2D structures to 3D form. 

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. 

Besides structure and substructure searches, Gmclin provides a special search strategy for coordiuation compouuds which is found in no other database the ligand search system, This superior search method gives access to coordination compounds from a completely different point of view it is possible to retrieve all coordination compounds with the same ligand environment, independently of the central atom or the empirical formula of the compound. 

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. 

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. 

Stmcture searching and display software are host-specific. The Softon Substmcture Search System (S4) was developed by the Beilstein Institute and Softon of Graefelfing Germany (50). It is a full stmcture and substmcture searching module. The S4 is used in-house by the Beilstein Institute and is operated by DIALOG. STN uses CAS ONLINE s messenger software for on-line stmcture searching of the Beilstein on-line database (51). 

Structure and Nomenclature Search System. This system links the collection of chemical databases found in the Chemical Information System (CIS), one of the first interactive systems for stmcture and substmcture searching. References from the separate files can be retrieved by SANSS using CAS Registry Numbers, and the database of stmctures may be searched for stmctures or substmctures. An adaptation of the SANSS software for substmcture searching has been incorporated in the Dmg Information System of the National Cancer Institute for its own use (54). 

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). 

The need for an overall and combined chemical structure and data search system became clear to us some time ago, and resulted in the decision to build CHIRBASE, a molecular-oriented factual database. The concept utilized in this database approach is related to the importance of molecular interactions in chiral recognition mechanisms. Solely a chemical information system permits the recognition of the molecular key fingerprints given by the new compound among thousands of fingerprints of known compounds available in a database. 

In this chapter, we will discuss the present status of CHIRBASE and describe the various ways in which two (2D) or three-dimensional (3D) chemical structure queries can be built and submitted to the searching system. In particular, the ability of this information system to locate and display neighboring compounds in which specified molecular fragments or partial structures are attached is one of the most important features because this is precisely the type of query that chemists are inclined to express and interpret the answers. Another aspect of the project has been concerned with the interdisciplinary use of CHIRBASE. We have attempted to produce a series of interactive tools that are designed to help the specialists or novices from different fields who have no particular expertise in chiral chromatography or in searching a chemical database. 

ChemIDplus. Published by the U.S. National Library of Medicine, ChemIDplus [62] is a web-based search system, http //chem.sis.nlm.nih.gov/ chemidplus/, that provides free access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. ChemIDplus also provides structure searching and direct links to biomedical resources at NLM and on the Internet. The database contains over 349,000 chemical records, over 56,000 of which include chemical structures, and is searchable by name, synonym, CAS registry number, molecular formula, classification code, locator code, and structure. 

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