Digital Briefs

Software

VEGA 1.5.1 freeware creates a bridge between most molecular software packages. It also has features that are useful for analyzing, displaying, and managing the 3-D structures of molecules. Among the new functions in this version are the capability to add hydrogens on the complete 3-D molecular editor and on the database engine. Other features are a Chem3D loader and Accelrys archive file (.arc) support in trajectory analysis. VEGA is written in high portable code (standard C language) and has been tested on the following operating systems: IRIX, Windows 9x/NT, Linux, FreeBSD, NetBSD, and AmigaOS. VEGA can be downloaded from http://www.ddl.unimi.it .

CombiMat 2.0 is a data management program for high-throughput experimentation (HTE) in materials science. CombiMat consists of an Oracle database and associated application modules. Features include library design, sample design, plate management, data entry and management, and project and work management. Project Explorer and Multiple Document Interface allow scientists to organize their work and interact intuitively with complicated and varied project data sets. The software is compatible with Windows. Accelrys, http://www.accelrys.com

Databases

RSC Journal Archive is a searchable database of more than 200,000 articles that were published in all Royal Society of Chemistry journals from 1841 to 1996. The articles are available via issue contents lists, from full-text searches of the PDF files, and by more specific searches of the bibliographic information. A Digital Object Identifier (DOI) has been assigned to each article. In addition, the references in the 1990–96 articles contain reference links to full text and CAS abstracts, where available, similar to those for the 1997–2003 articles. There is a one-time fee for permanent access to the archive. Royal Society of Chemistry, http://www.rsc.org

Online

MassSpectator is a mathematical method that locates and calculates the area beneath peaks from mass spectra using only reproducible mathematical operations and no user-selected parameters. It makes no assumptions about peak shape and requires no smoothing or preprocessing of the data. The method requires a background spectrum taken under the same conditions as the data. By automating the entire calculation process, MassSpectator saves time, makes it easy to work with massive data sets such as those used to study the functions of proteins, and eliminates errors or bias that might be introduced by manually translating mass spectrometry peaks into final chemical results. http://www.nist.gov/maldi

PHARMACEUTICAL APPLICATIONS

GASP (Genetic Algorithm Similarity Program) uses a genetic algorithm to discover the correspondence between functional groups in different molecules and the alignment of these groups in a common geometry. The program allows full conformational flexibility of ligands. The result is sets of overlaid molecules that serve as pharmacophore hypotheses. The program requires no advance knowledge of key functional groups or predefined correspondences between functional groups. GASP is accessible through the SYBYL molecular modeling environment, which runs on SGI and HP platforms. Tripos, http://www. tripos.com

Cerity Networked Data System for pharmaceutical quality assurance provides automated 3-D analysis, generic instrument control, and a spreadsheet-style custom calculator. The software enables pharmaceutical companies to evaluate and track the quality of raw and manufactured chemical compounds, and it enables scientists to use one computer to acquire and track data from up to 30 analytical instruments. Cerity implements the strict technical controls required by 21 CFR Part 11. The software is compatible with Windows. Agilent, http://www.agilent.com

DecisionSite for Lead Discovery allows users to examine the chemical and biological dimensions of their data and perform a wide array of numerical and structural analyses. The software provides chemical structure searching and retrieval of MDL Information Systems' ISIS databases, structure searching using CAS SciFinder, simplified access to high-throughput screening data stored in Oracle databases such as IDBS ActivityBase, and annotation searching in Current Drugs IDdb3. The software is supported on Windows. Spotfire, http://www.spotfire.com

MDL Plate Manager tracks, sorts, and manages large amounts of sample information generated in automated biopharmaceutical laboratories. The software resolves plate supply-chain bottlenecks, ensures sample integrity and data quality, and reduces cycle times and material inventories. By increasing laboratory throughput and streamlining workflow processes, Plate Manager helps organizations identify better drug candidates quickly and efficiently. The software is compatible with Windows. MDL, http://www. mdl.com

Digital Briefs is written by Janet Dodd, who can be reached at j_dodd@acs.org.