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Physical Chemistry


New Software And Websites For The Chemical Enterprise

by Janet Dodd
May 24, 2004 | APPEARED IN VOLUME 82, ISSUE 21

The following products were on display at the exposition during the American Chemical Society's national meeting in Anaheim, Calif. This is part 2; part 1 was published last month.


WABE software is useful in drug discovery for exploring the chemical space around a lead compound to elucidate candidates with improved drug profiles or novel scaffolds while avoiding patent conflict. Using a graph-invariant replacement algorithm, WABE quickly generates large numbers of isosteric analogs to a query molecule. Each heavy atom has the same hybridization as in the query molecule. The method resembles the process of chemical substitution--for example, carboxylate to amine--used in medicinal chemistry to create molecules having the same physical shape but varying in electrostatics. WABE is supported on various Linux, UNIX, Windows, and Mac OS X platforms. OpenEye,

ACD/ChemFolder 8.0

ACD/ChemFolder 8.0 provides enhanced searching, retrieving, and reporting capabilities that make it easy to effectively manage multitudes of chemical data from various instruments and analytical devices. The software provides users with the ability to manage thousands of separate files with chemical structures, reactions, and reports, as well as create and compare databases, predict chemical properties, and group and analyze data using advanced graphical presentation. ACD/ChemFolder contains a search system with an extensive range of both basic and advanced search capabilities for retrieving records by numerous properties and structural attributes, including substructure, structure similarity, stereoisomers, and subreactions. New to version 8.0 is the ability to search by case-sensitive text strings within user notes and data fields. Enhanced reporting capabilities make it possible to produce informative reports using a custom screen layout as a template. Users can print their records directly from ChemFolder, export them as Adobe PDF files, or convert them into ChemSketch reports. Advanced Chemistry Development,

ADF is a density functional software package for computational quantum chemistry. It enables researchers to accurately compute reaction paths and molecular properties in different chemical environments. ADF treats solvents, solids, proteins, transition metals, heavy elements, and electric and magnetic properties. ADF uses Slater functions, which resemble the true atomic orbitals more closely than Gaussian functions do. ADF also uses linear scaling and parallelization techniques to speed up the calculations significantly. The software package is supported on all major computer platforms (Windows, Mac OS X, Linux, and UNIX) and runs efficiently on Linux clusters. Scientific Computing & Modeling,

Ampac 8 is a semiempirical quantum mechanical program including a graphical user interface (GUI) that builds molecules and offers full visualization of results. Semiempirical methods include SAM1, AM1, MNDO, PM3, MNDO/C, MINDO/3, and MNDO/d. The software features simulated annealing for automated location of multiple minima, advanced transition-state-location methods, and configuration interaction for open-shell systems. Properties predicted are thermodynamic, electron spin resonance, vibrational spectra, electronic effects, and nonlinear optical effects. Solvated systems are treated by COSMO. The GUI features easy 3-D building, viewing, and manipulation and is completely compatible with Gaussian 03. The software is compatible with various Windows, Linux, and UNIX platforms. Semichem,

KnowItAll Informatics System V 3.1 contains ProfileIt, a new application that enables scientists to generate a comprehensive ADME/Tox profile that can be used to assess a compound's potential for advancement in pharmaceutical R&D. The program allows the user to view the results of all prediction models, such as blood-brain barrier permeability, log D, log P, mutagenicity, and plasma protein binding. Version 3.1 also offers a human intestinal<br > absorption prediction model to help researchers determine whether a drug candidate has a suitable oral absorption rate. This version incorporates enhanced data-mining capabilities, including the ability to color-code and assign weighting factors to records based on predefined rules for each property. The software is compatible with Windows platforms. Bio-Rad,

Chem 4-D Office 7.5 consists of six modules. Its drawing program creates all types of structures, reaction schemes, and flow charts. Nomenclator assigns systematic names to structures according to IUPAC nomenclature rules, and NamExpert converts IUPAC molecular names to 2-D structures in three styles: Kekulé, shorthand, and semistructural. The database organizes molecular structures, reactions, graphics, and chemical and biological information. Chem4D Graph creates multiline graphs of different styles and features nonlinear, linear, and response curve fitting and data analysis. Mass Calculator performs accurate element analysis for the interpretation of NMR and mass spectra. Chem 4-D is compatible with all Windows platforms, OS/2, and Macintosh Java. Cheminnovation,

Molecular Operating Environment (MOE)
Molecular Operating Environment (MOE)
Miner3D Enterprise 3.2.1
Miner3D Enterprise 3.2.1

Molecular Operating Environment (MOE) is a comprehensive software system for computer-assisted drug discovery and design. MOE 2004.03 features tools for bioinformatics, cheminformatics, high-throughput discovery, molecular modeling and simulations, protein modeling, and structure-based design. Enhancements in this version include the ability to search multiple databases and to design pharmacophore-based combinatorial libraries. Also, crystallographic visualization and electron density map visualization have been added. MOE runs on a variety of operating systems. Chemical Computing Group,

Miner3D Enterprise 3.2.1 is visual data-mining software for working with SQL databases, Access, and Excel. It converts data to graphical objects of corresponding size, color, position, shape, rotation, and transparency. Data series can be mapped on any of the properties and interactively scaled, zoomed, adjusted, or switched. Miner3D Access 3.2.1 produces randomly generated scatter, bar, or tile graphs. It features data mining, visual querying, cluster analysis, database navigation, and synthesized speech. Miner3D Excel, for advanced Excel users, includes interactive 3-D and 2-D visual data analysis, data mining, navigation, cherry-picking, and chart and report creation. Dimension 5, http:// 

FormRules automates the knowledge discovery process in developing new formulations, presenting the information as easy-to-understand rules and graphs. The software tries out a number of models to see which one fits the data best, then refines that model to improve the accuracy. Users can immediately see what formulation variables (ingredients or process conditions) affect each property. It can be applied to many formulation problems in pharmaceuticals, health and personal care, home care, paints and coatings, and adhesives. FormRules is Windows compatible. Intelligensys, http://

Leadscope Enterprise V 2.2 software enables scientists to explore datasets of chemical structures and similar information and relate the chemistry to other properties such as biological activity or toxicity. The Toxicity and Known Drugs databases provide capabilities for assessing the safety or pharmacology of compounds. This latest version includes new informatics wizards, a security system to manage access to data and results, new techniques for analyzing and visualizing the data, and enhancements to the reporting capabilities. Guided wizards help users import data and manage projects, browse projects, identify active classes, cluster structures, generate scaffolds, and create an R-Group table. The software runs on Windows 2000 or XP. Leadscope,



Emrys PathFinder, a database focused on providing detailed and reproducible methods for microwave synthesis, is now available as a Web service. Its components are PathFinder, for finding experimental conditions; Microwave Cookbook, for browsing a selection of popular reactions; Ask-a-Chemist, for communicating directly with support chemists; and Vapor Pressure Calculator, for automatic calculation of vapor pressure of common solvents. The site is regularly updated and now contains more than 3,600 reactions. Biotage/Personal Chemistry,


Organic Reactions is a comprehensive new database devoted exclusively to important synthetic reactions. It presents chemistry from a preparative point of view, with a focus on reaction limitations, interfering influences, the effects of chemical structure, and the selection of experimental conditions. Each reaction is presented with information about reaction conditions, products, and yields and is fully referenced to the primary literature. The database includes detailed procedures that illustrate the significant modifications of the chemical reaction and tables that include pertinent examples of the reaction. Wiley Interscience,


PsiPort Mass Directed Auto Purification software is a Web-based data review and data acquisition system for liquid chromatography and mass spectrometry operations. It was designed for automated compound isolation and purification for the life sciences and pharmaceutical discovery programs. The system uses an intuitive graphical user interface operating in Internet Explorer. The PsiPort browser enables users to view and track analytical results and fractions showing mass spectrum and associated UV, PDA, or ELSD results for each collected product. Shimadzu,

Reference Manager 11

Reference Manager 11 is bibliographic software for viewing and sharing reference collections. Its databases can be published on the Web, subject bibliographies can be created, references can be exchanged with colleagues, and users can connect to data visualization tools and support workgroups. Version 11 allows colleagues with a Web browser to access a Web publisher site to search and create reference lists or export references (RIS and XML formats). Users can instantly create a subject bibliography with topic headings. Reference Manager stores all of the cited reference data in a Word document, called a traveling library. With the new export traveling library feature, users can capture references directly from colleagues' papers. The software is designed for Windows 2000 and XP. Thomson/ISI ResearchSoft,

DiscoveryGate, a Web-based structure-searchable platform, is now available to students, faculty, and academic researchers. Combining 17 databases in chemistry, it integrates, indexes, and links scientific information to give immediate access to compounds and related data, reactions, original journal articles and patents, and authoritative reference works on synthetic methodologies. MDL,

Chemoventory2.0 is Web-based software that can be accessed over an existing intranet using any browser. It can be installed in any local machine or server and requires a Windows, Linux, or UNIX server and open-source products PHP, Apache Web server, and MySQL database. Its functionalities include managing chemicals, users, and groups; transferring chemicals from one user to another or to waste management; bulk uploading and exporting chemical lists; generating reports; managing material safety data sheet files; and printing bar codes. The software is available in two versions: Lite and standard. Lite has the functionality to manage chemicals but not users. The standard version has complete functionalities. Lite is ideal for labs with fewer than 10 chemists, is free, and can be downloaded without registration. Chemolink,

Digital Briefs is written by  Janet Dodd, who can be reached at



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