Digital Briefs

Software

Discovery Studio Modeling is designed for structural and computational chemists and biologists who need to perform expert-level modeling and simulations, crystallographic determinations, structure-based design (SBD), high-throughput functional annotation, and proteomic data storage tasks. DS Modeling 1.1 offers basic functionality focused on protein characterization, X-ray analysis, proteomic functional annotation, and homology modeling. DS Modeling 1.2-SBD offers structure-based design, including evaluation of ligand-protein interactions, de novo design, and docking. The software is for Windows-based personal computers. Accelrys, http://www.accelrys.com

ACD/Column Selector is a freeware column selection tool for Palm OS-based personal digital assistants (PDAs) that helps chromatographers select the optimal column. This tool enables the chromatographer to search a knowledge base of 135 characterized columns to locate those that have the properties best suited to the separation at hand. Each parameter can be targeted individually, so users can search for columns that have high coefficients for a certain term. This new tool can be downloaded from Advanced Chemistry Development, http://www.acdlabs.com/download/column_selector.html.

Marvin 3.2 and JChem 2.1 packages contain Java applications and software development tools for chemistry that run under Windows, Mac OS X, UNIX, and others. Marvin is a collection of Java tools for drawing, displaying, and characterizing chemical structures, substructures, and reactions. Some recent changes in Marvin are enhanced stereochemical representation and improved charge, logP, and pK_a calculations. JChem is a Java tool for the development of applications that allow for the search of mixed structural and nonstructural data. Some recent changes in JChem are a new JChem Cartridge for Oracle, enhanced performance of substructure search, especially in reactions, and substructure hit coloring and hit alignment. ChemAxon, http://www.chemaxon.com

Online

Information Retrieval in Chemistry offers access to chemistry-related information spanning a variety of chemistry disciplines, as well as information on other sciences. The Chemistry section is divided into more than 60 subsections corresponding to subdisciplines. Each subsection is further divided into areas such as Commercial Servers, Conferences, Databases, Educational Glossaries, Encyclopedias, Governmental Servers, Journals, Resources by Topic, and Societies/Organizations. http://macedonia.chem.demokritos.gr

Technical Computing

Mathcad 11 helps researchers calculate, graph, and communicate technical ideas. Patented electronic math technology lets scientists work with mathematical expressions using standard math notation but with the added ability to recalculate, view, present, and publish with ease, even to the Web. Mathcad integrates data across software and systems and enables users to distribute documents and collaborate across networks. Mathcad is available for Windows. Mathsoft, http://www.mathcad.com

Mathematica 5 is a comprehensive set of mathematical, scientific, engineering, and financial functions. The software handles complex symbolic calculations that can involve hundreds of thousands of terms; solves equations, differential equations, and minimization problems numerically or symbolically; does numerical modeling and simulations ranging from simple control systems to complex biological systems, chemical reactions, and environmental impact studies; and illustrates mathematical or scientific concepts for students at all levels. The software is available for Windows, Mac OS X, Linux, Solaris, and HP-UX. Wolfram Research, http://www.wolfram.com

Maple 9 includes a suite of differential equation solvers, intelligent symbolic algorithms integrated with numerical solvers, highly interactive visualization in 2-D and 3-D, and an intuitive programming language for rapid application development. The worksheet environment lets users create interactive technical documents and publish to the Web. The software is available for Windows, Mac OS X, Linux, and others. Maplesoft, http://www.maplesoft.com

FEMLAB 3.0 is an advanced software package for modeling and simulation of any physical process that can be described with partial differential equations (PDEs). It features high-performance state-of-the-art solvers that address extremely large problems and quickly yield accurate results. Working in a graphical interface, users choose from several ways to describe their problems in 1-D, 2-D, and 3-D. FEMLAB's PDE modeling capability enables it to link and solve coupled equations from arbitrary fields. The software runs under Windows, Linux, Solaris, and HP-UX. Comsol, http://www.comsol.com