CJACS database

A literature database well suited for obtaining the information we seek is the Current Journals of the American Chemical Society (CJACS) file. Like the CA file, CJACS is produced by the CAS and is searchable through the STN International network. The CJACS database has the advantages of being large (145,001 papers) and interdisciplinary, as well as covering some of the journals with the highest impact - on chemistry. The records in the database include not only abstracts, but also the full text of the articles and all the references and... 

Table 2 Journals Covered in the CJACS Database of the Chemical Abstracts Service...

Figure 1 The most frequently abstracted journals in MMCC during 1993. The bar graph shows the number of times each journal was abstracted. Journals that are also covered in the CJACS database are highlighted with dark gray. The numbers in parentheses are ISI impact values of each journal in 1992 (see Table 1) there is no value for Protein Science yet.

The SYBYL molecular modeling package is known for having the comparative molecular field analysis method for finding three-dimensional QSAR. 2 CJACS hits for CoMFA (Comparative Molecular Field Analysis) are plotted in Figure 20. CoMFA was mentioned in the CJACS database 9% as often as SYBYL, indicating that SYBYL is being used for many functions other than CoMFA. 

One of the most thorough ways of retrieving data from the literature is through searching databases of full articles. We find, from a detailed analysis of CAS s CJACS database, year-by-year increases in mention of many computational chemistry programs. Because of the sheer size of CJACS (145,001 articles), we expect it to be quite representative of the chemical literature as a whole. In addition, we have shown corroborative data from CAS s CJWILEY database and from the MMCC Results newsletter. 

A second smaller source of data on software usage is another database file available from the Chemical Abstracts Service. The file CJWILEY covers the full text of polymer journals (Table 3) published by John Wiley Sons. CJWILEY lists 8775 articles published in the seven-year period 1987—1993. Unfortunately, CJWILEY does not include Wiley s Journal of Computational Chemistry. By comparing findings from CJWILEY to the CJACS results, however, one can ascertain whether there are different patterns for modeling polymers versus modeling molecules in general. 

Figure 2 Number of papers added each year to the CJACS (Current Journals of the American Chemical Society) database file of the Chemical Abstracts Service. This file contains full text of each paper published. For purposes of this figure, computational chemistry papers are counted based on any mention of at least one of the 60 or so programs covered in this chapter. Among these programs are many of those most widely used, as well as a sampling of additional computational chemistry programs. The numbers of computational chemistry papers in this plot are lower bounds to the true numbers, however, because there are thousands of other programs in use.

Figure 10 Number of publications per year in the CJACS file mentioning CHARMM, AMBER, GROMOS, ECEPP, or OPLS. The academic version of CHARMM has the last M in uppercase, whereas the spelling CHARMm is used by MSI. Database searching is not case sensitive hence the developer s name was used as part of some of the queries. The search queries for each curve were (1) charmm and (simulation or modeling) and karplus, (2) amber and (simulation or modeling) and kollman (3) biomos or gromos, (4) ecepp, and (5) opls.

Some programs in the compound database management arena are compared in Figure 14. A software product that has controlled the lion s share of this market is MACCS." 4o CJACS mentions of REACCS, i which is a program for managing reaction databases are also plotted. ISIS, a recent front-end for accessing MACCS databases from desktop workstations in a distributed com-... 

The dominance of MDL in compound database management can be illustrated by pointing out that another company. Daylight Chemical Information Systems, which markets database management systems and compound databases, is mentioned in CJACS a total of five times. A Daylight software product called DAYMENUS is mentioned only once, and that was in 1992. THOR, the current name of the database management system, is cited in four papers. 

Figure 16 Yearly number of publications in the CJACS file mentioning the Cambridge Structural Database or the Protein Data Bank. The search queries for each curve were (1) protein w)data(w)bank, (2) xplor or x(w)plor, and (3) cam-bridge(w)structural(w)database. To minimize extraneous hits and to ensure have comparable curves, alternate names of the databases, such as CSD, Brookhaven, or PDB, were not used.

In contrast to the character string searches that were done on the full articles in the CJACS and CJWILEY databases, a different method of counting was used with MMCC Results. The newsletter usually indicates which of the... 

Figure 23 Total number of times three general purpose molecular modeling packages were mentioned in the CJACS and CJWILEY database files during the years 1987—1993. A logarithmic scale is used, to increase the visibility of the bars for the smaller data set.

Search for the piceol RN and cross-references to the database CJACS... 

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