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Physical Chemistry

DIGITAL BRIEFS

NEW SOFTWARE AND WEBSITES FOR THE CHEMICAL ENTERPRISE

by Janet Dodd
May 30, 2005 | APPEARED IN VOLUME 83, ISSUE 22

These products were on display at the exposition during the American Chemical Society's national meeting in San Diego. This is part 3.

Software


StructureSearch is a chemical substructure search engine packaged as a Java software development kit (SDK). It uses a proprietary multilevel search algorithm that compares the search target with dynamically built categorizations (meta data) of the dataset to be searched. Then, a very precise atom-path comparison provides accurate results quickly. Tools for building the meta data are included. Typical applications include e-commerce and enterprise workflow solutions. Synthematix, www.synthematix.com

Virtual NanoLab software uses atomic-scale simulations to understand nanostructures through virtual experiments. It makes it possible to compute the positions and electronic orbitals of atoms and molecules in arbitrary nanostructures. This software is a platform for modeling the physical and chemical processes that occur in nanoscale systems. The software describes not only the nanostructure, but also the coupling between the nanostructure and its environment. Virtual NanoLab runs on Linux and Windows. Atomistix, www.atomistix.com

Minitab 14 is statistical and graphical analysis software that includes features for basic statistics, regression analysis, analysis of variance, statistical process control, measurement systems analysis, multivariate analysis, and simulation and distributions. Release 14 includes capabilities for customizing menus and toolbars and for setting default behaviors for graphics, the data window, and the session window. The software includes a pictorial gallery of graphics such as scatter plots, histograms, charts, time-series plots, and 3-D graphs. The software runs under Windows. Minitab, www.minitab.com

The Amsterdam Density Functional package (ADF) is software for first-principles electronic structure calculations. It is particularly popular in the research areas of homogeneous and heterogeneous catalysis, inorganic chemistry, heavy-element chemistry, biochemistry, and various types of spectroscopy. The package includes the molecular ADF program, the periodic structure program BAND, and a graphical user interface for ADF. Based on density functional theory, ADF enables accurate treatment of transition-metal compounds with hundreds of atoms. A variety of Windows, Macintosh, UNIX, and Linux platforms are supported. Scientific Computing & Modeling, www.scm.com

DDDPlus (dose disintegration and dissolution) is a tool for formulation scientists that simulates the in vitro disintegration and dissolution of dosage forms. For new active ingredients, after a single calibration experiment, DDDPlus will predict how changes in formulation or in experimental parameters will affect dissolution rate. The software allows researchers to investigate the likely effects of altering various experimental parameters. The software is compatible with most Windows versions. Simulations Plus, www.simulations-plus.com

SciProof augments commonly used word processing programs with more than 250,000 scientific, biomedical, and chemical terms and allows users to add their own terms. It proofs for terms that should appear in italic type, such as genus and species names, and checks for subscripts and superscripts. It integrates with Windows. Thomson ResearchSoft, www.isiresearchsoft.com

Gold is a program for docking small molecules into protein binding sites. Silver is software that aids post-processing of Gold's virtual high-throughput screening results. Silver allows researchers to define a range of customizable descriptors that characterize how each docked ligand is interacting with the protein binding site. These descriptors, such as hydrogen bonding, accessible surface area, occupied volume, and simple properties, can then be computed and used to eliminate unpromising ligands and select suitable drug leads. Cambridge Crystallographic Data Centre, www.ccdc.cam.ac.uk

E-Notebook Ultra 9.0 streamlines daily record-keeping tasks of research scientists, maintains live chemical structures and data, documents work, and retrieves chemical information. It includes ChemDraw Std 9.0, ChemFinder Std 9.0, Chem3D Std 9.0, and the ChemINDEX database. It sets up as many project notebooks as needed, organized as desired. Notebook pages can include ChemDraw documents, Excel spreadsheets, Word documents, and spectral data. Pages can be searched by structure, keyword, date, and other data. E-Notebook runs on Windows platforms. CambridgeSoft, www.cambridgesoft.com

SingleCrystal 1.0 is a native Mac OS X program that works with CrystalMaker, reading from saved crystal files to simulate and display electron diffraction patterns on screen. Users can visualize entire sections of reciprocal space with the options of lattice or weighted-lattice display. SingleCrystal displays Miller indexes, mea sures distances and angles between diffraction spots, and displays the phases of reflections using color-coded spots. CrystalMaker, www.crystalmaker.com

WODCA (workbench for the organization of data for chemical applications) is a series of tools for the design of syntheses of organic compounds or combinatorial libraries in an interactive retrosynthetic approach. Target compounds can be "disconnected" into suitable precursor compounds. Catalogs of chemicals can be rapidly searched for available starting materials by various retrieval methods. Reaction databases can be used to find suitable synthesis reactions and conditions. Molecular Networks, www.mol-net.de

ACD/Combi NMR helps chemists perform complex tasks like verifying the structure of synthesized substances and estimating their quality by automatically determining a match factor between a structure and an NMR spectrum and by classifying the agreement as good, bad, or plausible. An automated data processor helps process, visualize, and publish data gathered by recording time-sampled NMR spectra to follow a reaction's progress. Combi NMR allows users to create a database by using import, drag-and-drop, or macro procedures and to verify the NMR spectrum-to-structure match in batch mode. The software is available for Windows. Advanced Chemistry Development, www.acdlabs.com

NMRPredict is a proton and carbon-13 prediction program. In proton NMR prediction, it uses a 3-D structure for its calculations. When multiple conformations are possible, it predicts a spectrum for every conformation. In carbon-13 NMR prediction, it uses a database of more than 100,000 verified data and a unique neural network algorithm to help predict molecules that are not well represented in the database. It differentiates its predictions based on the stereochemistry. The client runs under Windows XP or Windows 2000, and the server runs on Linux. Modgraph, www.modgraph.co.uk

ChemSite is a 3-D molecular modeling program that allows researchers to model, animate, render, and export 3-D molecular graphics for visualization and publication. Scientists can use molecular building blocks or atom-by-atom construction to visualize even the most complex structures as fully realized, space-filling entities. Movies of molecular dynamics simulations can be created. ChemSite images can be exported to any other Windows application. ChemInnovation Software, www.cheminnovation.com

Databases


AurStore is a comprehensive data-structuring system for the integration of proprietary biological and chemical information. Its Warehouse structure includes complementary Oracle objects and a database of biopharmaceutical information, such as drug interactions and therapeutic target families, for client data storage. Mapping and quality-control tools are part of its Management Software Suite. Aureus Pharma, www.aureus-pharma.com

Merged Markush Service (MMS) is a structure database of more than 1.6 million records. Each Markush record describes about 400 specific compounds, so MMS represents approximately 400 million single structures. MMS provides structure access to patent documents through Markush DARC software and is integrated with the PharmSearch and Derwent World Patents Index bibliographic files. Questel Orbit, www.questel.orbit.com

Web-Enabled


Integrity is an integrated drug discovery and development portal encompassing 10 knowledge areas, including chemistry, genomics, tissue engineering, pharmacodynamics, pharmacokinetics, and pathology. Integrity enables researchers to manage and correlate chemistry and genomics data with pharmacodynamics and pharmacokinetics data and with a knowledge base of disease entities. Its Highlights section is updated daily with news items and patents. Its database includes more than 200,000 compounds with demonstrated biological activity. Structure and text searching are fully integrated. Prous Science, www.prous.com

Aureka 9.2 allows users to search various bibliographic and specialized data fields of the full text of thousands of granted patents and published applications from all over the world. The PowerBrowse function enables users to review patents to decide which merit further analysis. Results can be analyzed with other tools in the Aureka platform, such as mining tools to evaluate the content and extract common themes. Patent images can be viewed with rotation, zoom, and print capabilities. Group access features and security settings allow users to share sensitive information within an organization. MicroPatent, www.micropat.com

FOR TEACHERS

Catalyst allows teachers to create a customized lab manual for introductory, general, environmental, analytical, physical, organic, and biological chemistry labs. Teachers can choose any combination of labs from a database of Prentice Hall, Pearson, and other contributors. The content of the available labs can be viewed online. After the desired labs are selected, a net price can be calculated, and an evaluation copy of the custom manual can be examined before an order is placed. Prentice Hall, www.prenhall.com

VOICE TO TYPE

NaturallySpeaking 8 provides a fast and easy way to turn speech into text. After about five minutes of simple training to allow the program to recognize your voice, you can launch any Windows-based application, including the full Microsoft Office Suite (Word, Excel, and Outlook Express), Word Perfect, AOL, and Internet Explorer. Users can surf the Web, write e-mails, even chat online by speaking into the computer. The program automatically inserts periods and commas and comes with a vocabulary of more than 250,000 standard and business terms. New words can be added. Frequently used blocks of text and graphics, such as name, title, and signature, can be inserted into documents with a voice command. The software runs on Windows. Voice Factor/PCS, www.voicefactor.com


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


 

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