Software, for computational chemistry

An updated, greatly enlarged compendium of software for molecular modeling appears as the Appendix. Programs that run on personal computers, minicomputers, workstations, mainframes, and supercomputers are listed together with some of their features. Telephone numbers and addresses of the vendors and/or developers are provided. To our knowledge, this is the most complete listing of sources of software for computational chemistry anywhere. 

An extensive compendium of software for computational chemistry appeared in Volume 7 of Reviews in Computational Chemistry. That compendium also had information about the Internet and the World Wide Web. We forego an appendix in this volume to allow more room for chapters. However, periodically in future volumes we will provide updated compendia. In the meantime, the compendium of Volume 7 can serve as a handy guide. 

The book is written for the users of such software, as they need to know what is really meant when we speak of the generation of molecular graphs, of substructures, of a goodlist of prescribed substructures, of overlapping substructures, of non-over-lapping substructures, of closed substructures, of substructure counts, of molecular descriptors, and so on. Otherwise, users will not be able to achieve the full potential of the software. It is also meant to provide documentation of the mathematical basics required for the designers of software for computational chemistry or chemoinformatics. 

This appendix is a brief and incomplete introduction to software useful computational chemistry for the PC. The order below is approximately the order in which the programs are used in the text. 

Software tools for computational chemistry are often based on empirical information. To use these tools, you need to understand how the technique is implemented and the nature of the database used to parameterize the method. You use this knowledge to determine the most appropriate tools for specific investigations and to define the limits of confidence in results. 

G. Additional Resource List for Computational Chemistry and Molecular Modeling Software... 

Rys, J.National Resource for Computer Chemistry Software Catalog. University of California -Berkeley Berkeley, CA, 1980 Vol. 1, program QH02... 

As the twentieth century came to a close, the job market for computational chemists had recovered from the 1992-1994 debacle. In fact, demand for computational chemists leaped to new highs each year in the second half of the 1990s [135]. Most of the new jobs were in industry, and most of these industrial jobs were at pharmaceutical or biopharmaceutical companies. As we noted at the beginning of this chapter, in 1960 there were essentially no computational chemists in industry. But 40 years later, perhaps well over half of all computational chemists were working in pharmaceutical laboratories. The outlook for computational chemistry is therefore very much linked to the health of the pharmaceutical industry itself. Forces that adversely affect pharmaceutical companies will have a negative effect on the scientists who work there as well as at auxiliary companies such as software vendors that develop programs and databases for use in drug discovery and development. 

Donald B. Boyd, Appendix Compendium of Software and Internet Tools for Computational Chemistry. 

Boyd DB. Compendium of software and Internet tools for computational chemistry. In Lipkowitz KB, Boyd DB, eds. Reviews in Computational Chemistry. Vol. 11. New York Wiley-VCH, 1997 373-399. 

Edwards continued to manage the day-to-day operations. In effect, Stan Hagstrom served as faculty advisor to QCPE. From April 1980 to April 1981, 451 programs were distributed to the United States, 212 to West Germany, 138 to Great Britain, 106 to Japan, and 77 to Switzerland. Also in 1981, the shortlived U.S. National Resource for Computational Chemistry (Lawrence Berkeley Laboratory, Berkeley, California) ceased operations and turned its software collection over to QCPE. 

We can glean other information from Figure 1. The little peak in 1985 and the modest one around 1989-1990 resulted from hiring at software companies catering to the pharmaceutical industry. A lucrative market developed for computational chemistry software written to meet the needs of the... 

With the integration of computational science into the daily routine of chemical, physical, and biological research efforts, it is not economical to devote resources to large-scale integration of operating and application software. The computational resources purchased today are now expected to come with shrink-wrap software, including computational chemistry applications, tuned for that resource and ready to run (i.e., a turnkey hardware and... 

Finally, we address a widely held opinion—that the growing commer-ciality of software for computer-aided chemistry would be the death knell of QCPE. This small, but important organization at Indiana University has been the mainstay since the early 1960s for distributing donated software at nominal cost to users all over the world. Most of the software is distributed as source code, which is rare among the commercial vendors. 

The number of programs for computational chemistry continues to evolve rapidly. In this compendium, we update and selectively expand the appendix that appeared in Volume 5 of Reviews in Computational Chemistry. The information is provided for the benefit of both developers and consumers of software. The contents are designed to provide a ready reference for researchers as well as newcomers to the field. The aim is to advance computer-aided chemistry by making the tools widely known. 

Drug discovery scientists have already adopted tools such as combinatorial chemistry synthesizers robotic systems for HTS and software packages for computational chemistry, molecular modeling, and design of experiments to identify lead compounds ( hits ). As the number of hits grows, there is a potential for process R D to become the bottleneck. The number... 

MOE Molecular Operating Environment is a software system designed specifically for computational chemistry... 

---