Databases retrieval

Most biochemical and/or molecular biology databases in the public domains are flat-file databases. Each entry of a database is given a unique identifier, i.e. an entry name and/or accession number so that it can be retrieved uniformly by the combination of the database name and the identifier. 

Two comprehensive integrated retrieval systems for nucleic acids and proteins, Entrez of NCBI, and SRS of EBI will be described briefly. The molecular biology database and retrieval system, Entrez (Schuler et al 1996) was developed at and maintained by NCBI of NIH to allow retrieval of biochemical data and bibliographic citation from its integrated databases. Entrez typically provides access to  

Entrez searches can be performed using one of two Internet-based interfaces. The first is a client-server implementation known as NetEntrez. This makes a direct connection to an NCBI computer. Because the client software resides on the user s machine, it is up to the user to obtain, install and maintain the software, downloading periodic updates as new features are introduced. The second implementation is over the World Wide Web and is known as WWW Entrez or WebEntrez (simply referred to as Entrez). This option makes use of available Web browsers (e.g., Netscape or Explorer) to deliver search results to the desktop. The Web allows the user to navigate by clicking on selected words in an entry. Furthermore, the Web implementation allows for the ability to link to external data sources. While the Web version is formatted as sequential pages, the Network version uses a series of windows with faster speed. The NCBI databases are, by far the most often accessed by biochemists and some of their searchable fields include plain text, author name, journal title, accession number, identity name (e.g., gene name, protein name, chemical substance name), EC number, sequence database keyword and medical subject heading. 

PubMed ] Entre I Human G enorhe. . I GefiBank I Map Viewer BLAST Search across databases I 

PubMed Central free, full text jaumal 

---

The ROSDAL (Representation of Organic Structures Description Arranged Linearly) syntax was developed by S. Welford, J. Barnard, and M.F. Lynch in 1985 for the Beilstein Institute. This line notation was intended to transmit structural information between the user and the Beilstein DIALOG system (Beilstein-Ohlme) during database retrieval queries and structure displays. This exchange of structure information by the ROSDAL ASCII character string is very fast. 

LMES (Lockheed Martin Energy Systems, Inc.). 1998. Material Safety Reference Sheet, Online database, retrieved 2/3/98. 

Fujibuchi, W., Goto, S., Migimatsu, H., Uchiyama, I., Ogiwara, A., Akiyama, Y., and Kanehisa, M. (1998). DBGET/LinkDB an Integrated Database Retrieval System. Pacific Symp. Biocomputing 98. R. B. Altman, A. K. Dunker, L. Hunter, and T. E. Klein, eds.), pp. 683-694, World Scientific, Singapore. 

Much useful reading material about computational chemistry is available. Some self-help information can be found at various websites. These can be located with any of the common search engines (database retrieval systems) that are convenient for finding resources on the World Wide Web. Once an individual is connected to the Internet, the search engines are free. A particularly fast, up-to-date, and comprehensive search engine is at http //www.google.com/. Queries can be in the form of words or... 

Figure 2,7. Query form of Access. Database retrieval is illustrated using Query form to retrieve amino acid database with Microsoft Access.

Retrieve one sequence (either DNA or protein) each from three major database retrieval systems—Entrez, SRS of EBI, and DBGet—and compare their outputs. 

The amino acid sequences of proteins and nucleotide sequences of DNA can be retrieved from the integrated database retrieval systems Entrez (http //... 

Tel. 617-873-2669, e-mail prophet-info bbn.com Molecular building, molecular mechanics, simulations, and display. Statistical and mathematical modeling and display. Sequence analysis. Structural and sequence database retrieval. UNIX workstations, such as Sun, VAX (Ultrix), DECstations, and Macintosh Ilfx (A/UX). 

Pln mo Atomic and Molecular Numerical Database Retrieval Display System)... 

Gold LS, Zeiger E,. Handbook of Carcinogenic Potency and Genotoxicity Databases. New York, NY CRC Press 1997. See also The Carcinogenic Potency Database. Retrieved from http //potency.berkeley.edu/index.html. Accessed March 18, 2009... 

RDF descriptors exhibit a series of unique properties that correlate well with the similarity of structure models. Thus, it would be possible to retrieve a similar molecular model from a descriptor database by selecting the most similar descriptor. It sounds strange to use again a database retrieval method to elucidate the structure, and the question lies at hand Why not directly use an infrared spectra database The answer is simple. Spectral library identification is extremely limited with respect to about 28 million chemical compounds reported in the literature and only about 150,000 spectra available in the largest commercial database. However, in most cases scientists work in a well-defined area of structural chemistry. Structure identification can then be restricted to special databases that already exist. The advantage of the prediction of a descriptor and a subsequent search in a descriptor database is that we can enhance the descriptor database easily with any arbitrary compound, whether or not a corresponding spectrum exists. Thus, the structure space can be enhanced arbitrarily, or extrapolated, whereas the spectrum space is limited. 

Molecular mechanics and display, statistical and mathematical modeling, database retrieval. 

Table 17.2. a Compilation of database-retrieved hexapeptides related to the peptide YLQTYH (residues 13 -18) of barnase. For each peptide a folding score is calculated as the product of fold pattern weight and similarity index. The cumulative scores for the four fold types are given at the bottom. The hexapeptide YLQTYH is the C-terminal end of an early formed helix [37] in barnase and adopts the secondary structure hhhhhn in the crystal [67]... 

Table 17.5. Compilation of database-retrieved hexapeptides matching patterns that are found again in helix 6 (a) and helix 7 (b), respectively, of Citrobacter freundii [69]. For each...

All rights reserved. Except as permitted under the United States Copyright Act, no part of this publication may be reproduced or distributed in any form or by any means, or stored in a database retrieval system, without prior written permission of the publisher. 

D Ligand-Based Virtual Screening 373 Table 13.1 Enrichment factors at 1% of database retrieval compared to random. 

ENVIRONMENTAL PROTECTION AGENCY 401 M Street SW, Washington DC 20460, (202) 260-4355. Administers federal environmental policies, establishes regulations, sponsors and conducts research, enforces regulations, and provides information on environmental subjects. Numerous branches based on type of environment, i.e., air, radiation, disposal, water, etc. Ten regional offices. On-line access points for database retrieval. Hazardous Waste and Cleanup Information Hotline same address, (800) 424-9346. 

---