SCIENCE/TECHNOLOGY
New Software Expands Role Of Molecular Modeling Technology • ACS show portrays a computational chemistry software industry undergoing change even as new products proliferate James H. Krieger, C&EN Washington
T
he mid-August news of a major merger in the computational chemistry software industry was still quite fresh when the fall exposition took to the floor at the American Chemical Society's national meeting late last month in Chicago. So it was much too soon for the merger to display any direct effect on the nature of the software technology making an appearance at the show. Nevertheless, the merger of Biosym Technologies, San Diego, and Molecular
Simulations Inc. (MSI), Burlington, Mass., was an added fillip to the software product introductions that have become a major activity at ACS expositions in recent years. The new offerings at last month's exposition exemplify a dynamic technology. It's a technology that despite a lackluster business climate remains a spawning ground for new products as it expands more broadly and deeply into various areas of application—for example, to materials as well as life sciences and to experimental chemists as well as computational specialists. Not only has an abundance of new products appeared in the computational and modeling area of the industry just since the last ACS exposition in April, but there are major new offerings in information management and in databases as well. And the influence of the Internet's World Wide Web (WWW) has become strongly evident. It was during the week before the exposition that Biosym and MSI announced they were joining forces to form a new company (C&EN, Aug. 28, page 12). Although of vastly smaller scale, the merger's significance to the computational chemistry software in-
Nearby booth signs at exposition betoken recent software industry merger. 30
SEPTEMBER 4,1995 C&EN
dustry is not unlike the effect within the chemical industry that can be imagined for a similar move by, say, Dow Chemical and DuPont. For one thing, the merger, which became effective Aug. 15, brings together what were in many ways two of the major competitors in molecular modeling software. MSI had been a privately held company. Biosym was a wholly owned subsidiary of Corning Inc. The new company will operate as an independent equity venture of Corning and the shareholders of MSI, with Corning owning about 55% of the outstanding shares. The new company is now by far the largest in the modeling and simulation sector of the computational chemistry software industry, with combined revenues in 1994 of more than $45 million. A new name is in the offing, but for now the company is operating as Biosym/MSI. It will have its headquarters in San Diego, with its European operations managed from Cambridge, England, which had been the European headquarters of MSI. "This merger creates a dynamic new company and signifies the beginning of a new era in this industry," says Michael J. Savage, former chief executive officer of MSI and now CEO of the new company. It is, he believes, "the most significant event in the history of the computational chemistry software industry." The principals in the merger see Biosym and MSI as having had complementary strengths. Savage notes, for example, that Biosym has had a particularly strong scientific base, especially with its industry consortia approach to software development. At the same time, he says, architectural elements of software design and broadscale deployment of the technology have been strengths of MSI. Savage thinks that integrating the two companies' technologies will be "surprisingly straightforward." For one thing, he says, the merger makes it possible to allow the company's scientists to
*
focus more strongly on new innovations. Almost immediately, he adds, Biosym/ MSI will be putting more emphasis on broader scale desktop deployment, with the aim of developing technology for the desktop that leverages the film's core competencies. Changes continuing at other firms are also helping to reshape the industry. Oxford Molecular Group, for example, has continued to deepen its involvement in applying an integrated molecular design approach to data management in drug design and development. That approach began to take shape a year ago with the U.K. company's acquisition of IntelliGenetics, a Mountain View, Calif., developer of software and database services for bioinformatics—a field that deals with genomic information, from gene discovery to DNA and protein sequence, structure, and function. The move expanded Oxford Molecular's product range beyond what had been essentially an assortment of software packages for use in pharmaceutical research. In January, Oxford Molecular added
Booth displays at exposition give an indication of active computational chemistry software development as applications continue to expand.
to its stable with the acquisition of CAChe Scientific, Beaverton, Ore., and its software tools that focused on the research chemist. As Oxford Molecular sees it, that move provided it with the means to use computational chemistry to integrate the drug discovery process from the bioinformatics (receptor) end to the chemoinformatics (ligand) end. A further significant move for Oxford Molecular came in late June with the announcement of a long-term agreement with the U.K.'s Glaxo Wellcome. Under that agreement, the two firms will codevelop a worldwide, fully integrated, and expandable software system aimed at expediting Glaxo Wellcome's drug discovery process. They will transfer the developed software to Oxford Molecular's commercial product line for support and future enhancements. In July, computer maker Silicon Graphics Inc. (SGI), Mountain View, Calif., joined the effort, agreeing to loan workstations and peripherals to the collaboration. Work on the project will be centered at Glaxo Wellcome's Research Triangle
Park, N.C., facility. Initially, the two companies will develop software for an integrated structure activity relationship (SAR) system. According to David E. Jackson, vice president of U.S. operations and deputy managing director at Oxford Molecular, Oxford is the first modeling software company to announce a program of this type with an end user. There is more to come. An announcement can be expected later this year, Jackson says, of an agreement with Glaxo Wellcome aimed at the entire drug development process, from gene discovery to computational chemistry. And further developments are likely later, since, as Jackson notes, a missing piece in the collaboration is that of a database partner. Meanwhile, Tripos Inc., St. Louis, has been strengthening the alliance it established earlier this year with Panlabs Inc., Bothell, Wash., according to Mark W. Schwartz, vice president of marketing. Schwartz thinks the collaboration, which involves Tripos in contract research services, makes the company unique. SEPTEMBER 4,1995 C&EN
31
SCIENCE/TECHNOLOGY Ο 'J
In the collaboration, Tripos, a compu tational chemistry software firm that fo cuses essentially on pharmaceuticals and biotechnology, provides design activities to create diverse libraries of chemicals. Panlabs, a contract research organization offering a range of services in pharma ceutical research, makes compounds with a high-throughput solution-phase synthesis method it developed. These compounds are then ready for pharma ceutical or biological screening by a cus tomer, or screening and further testing can be carried out by Panlabs. While mergers and collaborations are changing the nature as well as the face of the industry, development of the technology continues, with new soft ware products coming from just about all of the modeling software firms. In deed, some of those announced in Chi cago came from the former MSI and Biosym components of the now merged company. From MSI's point of view, the software developer's kit, C2«SDK, is the most im portant component of its newly intro duced product, version 2.0 of Cerius2, the company's molecular modeling environ ment and product line. "We're trying to create a completely open architecture, an open system, for the future of com putational chemistry," Savage says. As that statement implies, the Cerius2 approach is the result of MSI's particular product design philosophy aimed at bringing computational chemistry tools to the research chemist. Cerius2, intro duced about a year and a half ago, was a new-generation technology designed by the company to apply what it terms computational instruments. These are application programs that take molecu lar models, compute properties, and out put solutions to particular problems. Cerius2 is an environment something like that of Microsoft Windows, which
& >>- , , * ίi £>
32
SEPTEMBER 4,1995 C&EN
JsL
ft—gk*
f£
rot
1 CMNK*t
^J
A new chemistry resource goes on the web Home pages on the Internefs World Wide Web have become common place for many companies, particu larly those in the computational chemistry software industry. But a particularly wide-ranging one made its debut concurrently with the ACS exposition in Chicago. It is the Chemistry and Biological Sciences home page from Silicon Graphics Inc. (SGI), Mountain View, Calif. The page was conceived of as not simply a company product informa tion page but as a chemistry resource, according to Mark Berger, chemistry market manager at SGI. Calling up the home page (http://www.sgi.com/ ChemBio) provides a colorful screen with hyperlinks to many areas of in formation. Descriptions of company products are there, but a "Resources" linkage, for example, provides hyper links to a collection of technical pa pers and articles, images and VRML (virtual reality modeling language) sites for chemistry, professional asso ciation home pages, journal publica tion home pages, chemistry and life
provides a common convention for user interface commands, file formats, and program-to-program communications. C 2 · Visualizer, a core module, provides a comprehensive modeling environment for specific applications and access to ex ternal or in-house databases. Other core products—Cerius2 Builder Modules— enable the construction, display, and analysis of models of any type. For specific applications, MSI offers a range of modules called Cerius2 Work benches. These combine with the core modules to make up an integrated tool kit to support a user's particular research
On the cover One of the newer computational ap proaches to drug design is a method called Multiple Copy-Simultaneous Search (MCSS), developed by Har vard chemistry professor Martin Karplus and coworkers. The represen tation on the cover of this issue, mod eled using Cerius2 from Biosym/MSI, shows numerous chemical functional ities (N-methyl acetamide in green, acetic acid in yellow, methyl ammoni-
CfcwnHtri w * N*t«C«
