Digital Briefs

Software

(1) IdbsChemBook is a research management program to support and simplify the day-to-day work of medicinal and synthetic chemists. Part of the E-WorkBook suite, ChemBook allows chemists to ensure that all research findings are stored securely and completely with any contextual data along with reaction details, Microsoft Office documents, and Web links. The program also features a reaction-drawing tool, stoichiometry calculations, definable structure-rendering options (bond lengths, stereochemistry, aromatic representations, atom colors, and default font size), structure refinement in situ, single and bulk compound registration, parallel synthesis library enumeration, and industry-standard chemistry searching (SSS, exact, similarity, reaction transformation, product/reactant, and more). ChemBook runs on Windows (XP and Vista) and requires an Oracle database and Windows application server. idbs, www.idbs.com

De Novo Drug Design Suite is a portfolio of tools for virtual de novo drug design and library generation. Consisting of four tools, the suite is versatile and simple to use. The first tool, CoLibri, permits the creation, management, and manipulation of ligand fragments, including the capability to assemble gigantic fragment collections from multiple sources while removing duplicate fragments. Compounds created from CoLibri's fragment spaces can be searched by using the second tool, FTrees-FS, a ligand-based alignment and similarity search engine. Alternatively, a novel structure-based design method, FlexNovo, based on the established docking engine of FlexX, is also part of the suite. Recore, the final tool, replaces user-defined central elements of known bioactive molecules to generate novel scaffolds in 3-D. The software is supported on Linux (other platforms available on request). BioSolveIT, www.biosolveit.com

UN-SCAN-IT v5.2 is an upgrade to a popular software used for digitizing graphs. The new version now automatically converts scanned graphs to (x,y) data through a drag-and-drop interface, colored data-line follower, improved grid-line filters, and a graphical (x,y) data eraser. The software works with any scanner, digital camera, or image-input device, and it can be used to digitize journal graphs, strip-chart output, old graphs, or any other hard-copy graph. The software allows the user to compare and analyze data from graphs that are on different scales; analyze and store hard-copy output in digital (x,y) form on disc; and export data to other spreadsheet, data-analysis, and graphics programs. Other upgrades include the speed to analyze up to 10,000 data points per minute; the memory to store up to 25,000 data points per file; and the flexibility to digitize JPG, TIFF, BMP, GIF, TGA, PICT, PCX, and other image formats. UN-SCAN-IT v5.2 runs on Mac OS X and Windows. Silk Scientific, www.silkscientific.com/home.htm

(2) COSMOmic is a software application that is based on the COSMO-RS theory (which provides novel access to solvation questions) that derives the thermophysical behavior of liquids from quantum mechanical density functional theory calculations. The software describes micelles or biomembranes as liquid layers, and it determines partition coefficients of solutes efficiently and without the need to fit additional parameters. COSMOmic offers applications to analyze and validate partition coefficients, probability distributions, free-energy profiles, neutral and ionic solutes, spherical micelles, and lamellar micelles such as phospholipid biomembranes. Further applications include the determination of permeability coefficients of solutes through membranes and of Flory-Huggins-like parameters that can serve as input for meso-scale applications such as dissipative particle dynamics. COSMOmic runs on Windows (XP and Vista) and Linux. CAChe Research, www.cacheresearch.com/cosmo.html