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Physical Chemistry

Digital Briefs


by Janet Dodd
March 28, 2005 | A version of this story appeared in Volume 83, Issue 13

The following products were on display at the exposition during the American Chemical Society's national meeting in San Diego. This is part 1; part 2 will be published next month.


Accord Enterprise Informatics (AEI) 6.0 is an Oracle-based information management solution that enables storage, search, and retrieval of corporate chemical and biological screening and inventory data. It is delivered via a range of infrastructural and task-focused products, all of which benefit from new features and performance enhancements. These include reaction registration; Markush query support; and faster querying, reporting, structure searching, and registration. AEI 6.0 runs on Solaris 8 and 9 and Redhat Linux E.S. 2.1 and 3.0; Windows 2000 and XP. 8i and 9i versions of Oracle Standard and Oracle Enterprise are supported. Accelrys,

SpartanModel is an electronic model kit designed to replace the existing plastic model kits used in organic chemistry education. Making use of computer technology, this stand-alone molecular-modeling program provides chemistry students with unique tools for building and visualizing molecules. The program also provides structure refinements using molecular mechanics calculations and includes access to a database comprising several thousand common organic molecules. SpartanModel supports modern Windows and Macintosh platforms. Wavefunction,

Phase is a complete package for pharmacophore modeling that offers scientists a high level of control at each step. Phase intuitively guides the user via an easily mastered step-by-step interface through the process of finding and evaluating a pharmacophore model, creating a QSAR hypothesis, and searching a 3-D database. The software extensively explores the conformational space and allows customization of feature definition and scoring. Phase supports parallel processing such that computationally intensive steps can be executed on multiple processors to enhance throughput. The software is compatible with Linux and SGI IRIX systems. Schrödinger,

EON 1.1 screens databases of molecules for shape and electrostatic similarity to a lead compound and thereby facilitate lead generation and library design for drug discovery. EON compares electrostatic potential fields throughout space around molecules and determines Tanimoto and Tversky measures as rigorous metrics for the comparisons, so that a database can be quickly sorted by similarity to the query compound. In a typical workflow, with a query molecule known to be active against a target protein, ROCS is used to screen multiconformer corporate databases. This process, yielding compounds with both similar shape and similar electrostatics, can be run on million-compound libraries in a day on a single processor. The software is available for Linux, Windows, Mac, SGI, HP/Compaq, IBM, and SUN versions of UNIX. OpenEye Scientific Software,

KnowItAll Informatics System Version 5.0 features advanced multitechnique database searching that enables users to define searches in multiple spectral techniques concurrently in a single software platform--even across multiple databases--and view consolidated results. Traditional spectral search and analysis software programs focus on one spectral technique at a time, but KnowItAll gives scientists who analyze samples using multiple spectral techniques the ability to combine all spectral information available to yield a single search result. The system requires Windows 2000 or XP. Bio-Rad,

Conflex5 has the capability to completely search the conformational space of a flexible molecule to find every optimal structure of chemically significant conformers. The software uses strategies such as downstream/reservoir-filling, a variable search limit, three modes of perturbation (unique corner flap, edge flip, and stepwise rotation), and precheck. Conflex5 calculation results can be output in a variety of formats, permitting their use in applications for ab initio calculations or visualization applications. Operating systems supported are Mac OS X 10.2 and up, Redhat Linux 7.1 and up, and Windows XP. Conflex,

Digital Briefs is written by Janet Dodd , who can be reached at



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