Software for Molecular Modeling

Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285 

The compendium is provided as a service to both developers and consumers of software. The contents are designed to help researchers stay abreast of new code and to introduce newcomers to sources and other useful information. The aim is to advance the field by making the tools widely known. 

As used here and expounded on in Volume 1, molecular modeling refers to the generation, manipulation, and/or representation of realistic molecular structures and associated physicochemical properties. The terms molecular modeling and computational chemistry are used interchangeably. Not only should many techniques be included under the umbrella of molecular model- 

Reviews in Computational Chemistry, Volume V Kenny B. Lipkowitz and Donald B. Boyd, Editors VCH Publishers, Inc. New York, 1994 

For each software package, we give a brief description, the address and telephone number of the supplier, and other pertinent information, such as when a vendor offers more than one program pertinent to molecular modeling. The descriptions are concise overviews, not reviews, and an effort has been made to free the descriptions of commercial embellishments. When possible, a toll-free (U.S.A.) telephone number and/or an electronic mail address is given to make it easier to communicate with the supplier. 

Department of Chemistry, Indiana University-Purdue University at Indianapolis (lUPUI), Indianapolis, Indiana 46202-3274 

For each software package, we give a brief description, the address and telephone number of the supplier, and other pertinent information (e.g., other 

Prices of software, which range from essentially free to more than 100,000 (U.S.), are not included because they are subject to change and to specific conditions of distribution. In some cases, particularly with respect to QCPE (Indiana University, Bloomington), significant software, which has been validated with respect to expected output, can be obtained at minimal cost. With so much excellent software and so many suppliers now vying for attention, the consumer of software products is in a good position to explore all possibilities. 

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Most chemists want to avoid the paper-and-pencil type of work that theoretical chemistry in its truest form entails. However, keep in mind that it is precisely for this kind of painstaking and exacting research that many Nobel prizes have been awarded. This book will focus almost exclusively on the knowledge needed to effectively use existing computer software for molecular modeling. 

Donald B. Boyd, Appendix Compendium of Software for Molecular Modeling. 

Figure 5 The crystal structures for SEB and TSST-1. These structures were constructed by using data provided by Entrez s 3-D database and software for molecular modeling. Primary references for SEB and TSST-1 crystai structures are Papageorgiou etal. and Prasad ef respectiveiy.

Published FF parameters for MM (Jalaie and Lipkowitz, 2000 Osawa and Lip-kowitz, 1995) and software for molecular modeling (Boyd, 1995) have been compiled. Some of the MM programs applicable to molecular modeling of biomolecules are listed in Table 14.1. 

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. 

How then does one measure the usefulness of software for molecular modeling Certainly, use of the software contributes to the understanding of molecules and their properties. It helps people think about how molecules look, act, interact, and react. Still, it is difficult to quantitate understanding. Alternatively, since many of the programs are used in conjunction with computer-aided molecular design efforts, one could try to measure how many compounds in the development pipeline were discovered with some assistance by computational research.However, this too is difficult to quantitate objectively and comprehensively. 

Eds., VCH Publishers, New York, 1994, Appendix, pp. 381-428. Compendium of Software for Molecular Modeling. 

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