Digital Briefs

Software

FRED 2.1 is the latest release of an accurate and fast docking program. For every ligand, FRED exhaustively searches all possible conformations within a protein active site, filtering for shape complementarity and pharmacophoric features. It evaluates its findings via several scoring functions, including ChemScore, ScreenScore, and ChemGauss. A systematic search algorithm predicts binding modes in a reproducible manner. FRED docks about a dozen ligand conformers per second per processor and performs constrained docking, wherein certain pharmacophoric features are guaranteed to be in specific regions of the active site to allow scientists to take advantage of known structure-activity relationships. The software runs on Linux, Windows, Mac OS X, HP/Compaq, IBM, SGI, and SUN UNIX. OpenEye Scientific Software, www.eyesopen.com

RefViz Version 2 is data visualization and analysis software that enables users to search multiple online databases simultaneously. It analyzes large numbers of references by thematic content and presents an overview of the main topics. The software automatically eliminates duplicate references from different online databases. It downloads large result sets in background mode and informs the user when it's finished. An expanded thesaurus provides the ability to identify equivalent terms. The software is available for Mac OS X and Windows. Thomson Research-Soft, www.researchsoft.com

IRIS Explorer 5.2 is a system for visualization of scientific data with a visual programming interface that enables users to create applications from software building blocks, also called modules. Researchers can try several ways to convert numerical data into different types of pictures. The IRIS Explorer distribution includes hundreds of modules, and researchers can add new functions by writing their own modules, using the development tools provi ded. The 3-D visualizations created can be manipulated in real time. IRIS Explorer runs on Windows, Linux, SGI, Sun, HP, and IBM systems and is now available on the Mac OS X platform. Numerical Algorithm Group, www.nag.com

GRINSP for Windows Version 1.00 (geometrically restrained inorganic structure prediction) is a Monte Carlo code in Fortran for the prediction of inorganic structures built up from defined polyhedra. The software produces structure candidates for N = 3, 4, 5, or 6 in binary compounds, in ternary compounds mixing tetrahedra and octahedra, and in triangles with octahedra or tetrahedra. The current limitation is that polyhedra be exclusively connected by corners. A. Le Bail, sdpd.univ-lemans.fr/grinsp

Quantemol-N is software for predicting how molecules and electrons interact on a quantum subatomic level. It yields data on collision cross-sections, excitation cross-sections, and rates for electron collisions with user-defined molecules. Applications include designing plasma-etching processes for semiconductors, controlling the action of lasers, understanding radiation damage in biological tissue, and modeling the behavior of Earth's ionosphere. Quantemol, www.quantemol.com

STN Express with Discover, Analysis Edition, Version 8.0, allows information professionals to present search results in reports or tables and also boosts the ability to search, analyze, visualize, and review scientific information. The Variable Group (R-Group) Analysis Tool can analyze multicomponent chemical substances. Researchers can preview substances to ensure the inclusion of relevant structures from the CAS Registry. The software runs under Windows. Chemical Abstracts Service, www.cas.org

Databases

The Biomolecular Interaction Network Database (BIND) Version 3.7 is available to academic, government, and commercial scientists for free. BIND offers data that span molecular interactions between proteins, small molecules, and nucleic acids as well as genetic interaction networks in a standardized format. Tabbed search results are divided into interaction, complex, and pathway categories. OntoGlyph summaries provide researchers with a rapid view of functional, binding, and subcellular localization features. Small-molecule browse upgrades display key small-molecule information such as LD₅₀, log P values, and melting and boiling points. Blueprint, www.blueprint.org

Online

SpecInfo is a collection of more than 434,000 curated spectra, now available online. It allows users to view, predict, and search spectra in three specialized fields: infrared, nuclear magnetic resonance, and mass spectrometry. Users can search by structure, substructure, complete spectra, individual spectral features, chemical names, and molecular properties. Each entry includes chemical name, molecular formula, molecular weight, literature reference, solvent, standard, and measurement conditions. Wiley InterScience, www.interscience.wiley.com

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