CJACS

Ceramic Abstracts Chemical Engineering and Biotechnology Abstract (CEBA) Chemical Journals of the American Chemical Society (CJACS)... 

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...

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 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.

RESULTS FROM THE CJACS FILE ONWARD AND UPWARD... 

Results from the CJACS File Onward and Upward 325... 

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 3 Computational chemistry papers (Figure 2) in the CJACS file as a percentage of the total number of articles in CJACS the percentage has increased each year. Note that 1989 s percentage does not show a large jump like in 1988 and 1990. This is because the use of Gaussian was flat in 1989 with respect to 1988, while mentions of MOPAC and QCPE actually dipped in 1989, as seen later (Figures 12, 13, and 22).

PCMODEL are supported by developers at Columbia University and Indiana University, respectively. Neither is backed by a large marketing or sales force. Yet each has enjoyed noteworthy success in terms of being used in publications. Also plotted are CJACS hits of Chemical Design Ltd., which supports Chem-X, and Serena Software, which has PCMODEL. Literature mention of the Chem-X package exceeded that of Insight/Discover, SYBYL, and Quanta/CHARMm for at least one year in the 1980s, but publications from users of Chem-X have not kept up and have fluctuated around the same level in the last few years. 

Figure 5 Yearly number of publications in the CJACS file mentioning four vendor...

Figure 6 Total number of papers in the 12-year period covered by CJACS for three molecular modeling software vendors. Abbreviations are MSI for Molecular Simulations Inc. and CMD for Cambridge Molecular Design. These searches were structured to identify the vendors by the city in which their headquarters is (or was) located. For MSI, three cities were used. The queries were (1) tripos and st(w)louis, (2) biosym and san(w)diego, and (3a) biodesign and pasadena, (3b) polygen and Waltham, (3c) (molecular(w)simulations(w)inc and waltham) or (molecular(w)sim-ulations(w)inc and burlington), (3d) cambridge(w)molecular(w)design.

Figure 7 Yearly number of publications in the CJACS file mentioning three other molecular modeling programs. CDL is Chemical Design Ltd. The search queries for the curves were (1) macromodel, (2) pcmodel or serena, (3) chemx or chem(w)x or chemical(w)design(w)ltd or chemical(w)design(w)limited, (4) serena, and (5) chemi-cal(w)design(w)ltd or chemical(w)design(w)limited.

Two other software packages with molecular mechanics capability are MOBY o and PROPHET. For the entire period covered by CJACS through 1993, a search for MOBY yielded four papers PROPHET, which has been around since the early 1980s, is named in five. 

Figure 9 Yearly number of publications in the CJACS file related to MM2, MM3, or MMX. The search queries for each curve were (1) mm2 and (force(w)field or molecular(w)mechanics), (2) (mm2 or mm3) and allinger, (3) mm3 and (force(w)field or molecular(w)mechanics), (4) (mmx or mm(w)x) and (force(w)field or molecular(w)mechanics), and (5) (mm2 or mm3) and (technical(w)utilization or tripos or molecular(w)design).

Results from the CJACS Fite Onward and Upward 333... 

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.

Figure 12 Number of publications per year in the CJACS file mentioning semiem-pirical MO programs MOPAC, AMPAC, AMSOL, or ZINDO. The search queries for each curve were (1) mopac, (2) ampac, (3) amsol, and (4) zindo.

CJACS hits for other ab initio programs in Figure 13 include HONDO, GAMESS, and CADPAC. All these were developed in the era of nongraphical input/output. DMol is a program for density functional computations. ... 

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-... 

Figure 15 Number of publications per year in the CJACS file mentioning LHASA. The search query was lhasa.

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. 

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