Databases and Programs

In conclusion, we note that most studies to date have considered only small molecules with contributions to the field being principally from medicinal chemists and information scientists. However, recent papers on substructure searching in macromolecules indicate that protein crystallographers and molecular biologists are now also getting involved. We believe that the interactions between the disparate disciplines will prove fruitful in the further development of techniques for three-dimensional substructure searching of both small and large molecules. 

Cambridge Struaural Database System, CAVEAT Prof. O. Kennard OBE FRS Cambridge Crystallographic Data Centre University Chemical Laboratory Lensfield Road 

Quantum Chemistry Program Exchange Chemistry Department Indiana University Bloomington, Indiana 47401 

The authors especially appreciate the contributions of the following researchers F. H. Allen, P. M. Dean, T. Esaki, P. Gund, A. J. Hopfinger, M. Johnson, R. P. Sheridan, and D. H. Smith. 

Bernstein, and T. F. Koetzle, in The Role of Data in Scientific Progress. P. S. Glaeser, Ed., Elsevier, New York, 1985. The Protein Data Bank. 

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ACD database and program MACCS supplied by Molecular Design Ltd. San Leandro, CA. 3-D-database programs were not available to us... 

Chapter 9—In Silico siRNA Design Leon reviews the basic concepts of siRNA design and discusses how siRNA methodologies are being used in research and as therapeutic tools. He also gives a brief overview of the public and commercial databases and programs available and includes useful destinations on the Web where you can find related information. 

Another problem with the choice of descriptors is accessibility. Some types of proprietary parameters are only available through the licensing of commercial software. There are, however, some web-based resources, such as Chembench (http //chembench.mml.unc.edu) and the Virtual Computational Chemistry Laboratory (www.vcclab.org) which both provide not only descriptor calculation facilities, but also access to statistical analysis routines. The molecular descriptors website (www.moleculardescriptors.eu) and QSAR world websites (www.qsarworld.com/qsar-web-based-programs.php) also provide useful links to resources such as databases and programs. 

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. 

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. 

MDL Information Systems, Inc. MDL provides modular software systems for managing chemical information, as weU as related molecular and reaction databases for use with the software. MDL s database management programs, MACCS-II and REACCS, provide access to compound and reaction databases and also have the capabiHty to manage user-created databases (37). Although MDL is not considered to be an on-line database vendor, it is mentioned here because of the value of its information products and services to the chemical industry. 

ISI is available in hard copy and electronically at EPA s headquarters and regional Hbraries, and through the National Technical Information Service (NTIS). The electronic form may be installed on IBM PC-compatible computers or placed on local area networks, and mn under Microsoft WINDOWS or WordPerfect s Library program. The Macintosh version is no longer available. The 1993 update will include the ISI hardcopy, PC disks, and the PC system user manual. EPA also pubHshes ACCESS EPA, which provides sources of information, databases, and pubHcations within the EPA. Chapter 5 of that pubhcation includes important environmental databases in air and soHd waste, pesticides and toxic substances, water, and cross-program (110). EPA also provides databases accessible through EPA Hbraries, which describe the private EPA and commercial databases available to Hbrary users (111). 

Mass storage device. Typically, fixed-head hard disk drives are used to store ac tive data, including on-line and historical databases and non-memory-resident programs. Memory-resident programs are stored to allow loading at system startups. The tape drives are used for archives and backups. 

Stein, S. E., J. M. Rukkers, and R. L. Brown, 1991. NIST Standard Reference Database 25, The NIST Structures and Properties Database and Estimation Program, Version 1.2, September, NIST. 

These reports were in addition to the internal reporting for OSHA PSM and various local or state requirements. While Quality Chemical had long ago consolidated a number of these programs, there were still four different accident/incident reporting systems—one for external reporting of releases, one for external reporting of injuries and other nonrelease events, one for a corporate-wide database and one for each site itself. 

Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ, Gapped BLAST and PSI-BLAST a new generation of protein database search programs. Nucleic Acids Res 1997 25 3389-402. 

Below we describe three examples of frameworks that use the Best in Class approach including another US EPA DfE Program called the Formulator Program, the CleanCredients database and SC Johnson s GreenList . 

In this program the oratabs libref allows all of the tables found in that Oracle data instance to be treated like SAS data sets. This is a simple and fast way of accessing relational databases, and it requires no knowledge of SQL to implement. 

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