software/online briefs The following products were on display at the exposition during the American Chemical Society's national meeting last month in Washington, D.C.
• Software 301 ACD/Name generates accurate systematic names according to IUPAC and IUMBM recommendations on nomenclature of organic chemistry for almost any organic structure and selected classes of natural products and biochemical, orga-
ly or imported directly from instruments or robotic systems. ActivityBase allows any type of sample to be registered: discrete compounds, combinatorial libraries, mixtures, formulations, enzymes, cell lines, and DNA sequences. A wide variety of information can be stored against a sample, such as physical properties (molecular weight, formula, log P, and solubility); structure; spectra (NMR, HPLC, and mass); documents (gel images and cell profiles); sample location; and inventory information (current quantities and volumes). ActivityBase integrates seamlessly with Excel, Word, and Oracle. IDBS
nometallic, and inorganic compounds. ACD/Name allows chemists to use the ChemSketch interface to sketch in the molecular structure, ion, or set of structures or ions for naming; assign systematic numbers to all atoms in the structure; assign stereo descriptors to chiral centers and double bonds; assign structural fragments to the corresponding portions in the generated name and vice versa; customize name-generation preferences; store and load generated names with structures from special history files; import structures from databases and automatically name them; and export structures and names. The software runs under Windows 95, 98, 2000, and NT 4. Advanced Chemistry Development
303 Ampac offers tools for studying chemical reactions and structures. It is a semiempirical quantum mechanical program that includes a graphical user interface (GUI) to build molecules. It offers full visualization of results. The computational module provides a variety of semiempirical methods that allow computation of the properties of molecules in aqueous solutions or any organic solvent; simulated annealing for location of multiple minima automatically; advanced transition-state location methods; and property prediction including thermodynamic, electron spin resonance, vibrational spectra, and electronic effects. The GUI provides 3-D building, viewing, and manipulation via a variety of predefined chemical building blocks (rings, groups, amino acids, and ligands); is compatible with Gaussian 98; displays predicted vibrational spectra; and animates vibrational modes. The software supports various platforms, including Windows, Silicon Graphics, Sun, and Linux. Semichem
302 ActivityBase 4 is an integrated software solution for the management of drug discovery workflow, data capture, analysis, and decision-making. With ActivityBase, it is possible to manage virtually all of the steps in a testing program. With the chemistry management capabilities, scientists can register and interrogate test sample data (including chemical structures). Raw data can be entered manual-
304 Cranium is a software package capable of predicting values for more than 20 physical properties. Estimates are generated for both pure components and mixtures (up to five components). The user draws a compound's molecular structure or enters its composition, and Cranium automatically analyzes the structure for important functional groups, selects the best estimation technique, retrieves any
For Students and Teachers 324 Thinkwell's Chemistry consists of a CDROM set and customized website working in tandem to supplement or replace print textbooks. The CD-ROM set contains the video tutorials. The customized website contains accompanying illustrated notes, exercise problems, animations, and a threaded discussion forum. Thinkwell customizes the material to follow the sequence of each teacher's syllabus. The online testing system allows practice and quizzing and also provides reports on student progress and performance. Thinkwell.com 46
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CHEMISTRY
required property data, and provides an accurate estimate. Cranium's system knowledge base contains data on more than 600 pure components, 70 mixtures, and 80 physical-property estimation techniques. The software is Windows compatible. Molecular Knowledge 305 CrossFire 2000 is a client-server system for navigating two of the world's largest electronic collections of chemical data: CrossFire Beilstein, which contains data describing the preparation and properties of more than 8 million known organic chemical compounds, and CrossFire Gmelin, which contains more than 1.4 million inorganic and organometallic compounds. Search options enable researchers to conduct complex, fact-based searches over the two databases. A key capability is "science hopping," which enables scientists to "jump" between the CrossFire client and virtually any application. CrossFire also includes AutoNom Standard, an application that generates IUPAC chemical names directly from graphical structures created in CrossFire's structure editor or in ISIS/Draw. Users can select either the structure editor or ISIS/Draw as their preferred drawing tool. MDL 306 DayCart provides tools that enable Oracle 8i database servers to understand chemical information. DayCart supports the storage, searching, and retrieval of 2-D and 3-D molecules, reactions, and mixtures via the SMILES language. Operations provided include high-performance searching of full structure, substructure, superstructure, similarity, and other structural operations. Daylight 307 GaussView is a graphical user interface for Gaussian 98. Windows-based GaussView enables users to construct molecular systems of interest quickly and efficiently using its molecule-building facility.
Gaussian calculations can be set up and run right from the interface. A variety of results can be inspected graphically via advanced visualization facilities. GaussView incorporates a molecule builder that enables even very large molecules to be rapidly sketched in and then examined in three dimensions. It allows users to do the following: build molecules by atom, ring, group, and amino acid; import molecules from other sources by simply opening them with GaussView; examine or modify any structure parameter by clicking on the associated atoms and using an intuitive dialogue box; rotate molecules in three dimensions;
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software/online briefs and view molecules in a variety of customizable display modes—wireframe, tubes, and ball and stick. Gaussian 308 HyperChem is a molecular modeling program that unites 3-D visualization and animation with quantum chemical calculations, molecular mechanics, and dynamics. HyperChem allows users to build molecules and convert rough sketches into 3-D structures. Computational methods available with HyperChem include ab initio, semiempirical, and molecular mechanics. Release 6 allows users to calculate properties such as the vibrational spectra or the orbitals of a molecule and save the results as an HTML file that can be placed on a website. Because the files are dynamic, the molecules can be rotated, the orbitals varied, or the vibrational modes animated. The software is compatible with Windows 95, 98, NT, and 2000 operating systems. Hypercube 309 Materials Visualizer provides the tools required to construct graphical models of molecules, crystalline materials, and polymers and to manipulate, view, and analyze these models. The program also handles graph, tabular, and textual
data. It can be used to support Materials Studio products or it can be run standalone. Materials Visualizer allows users to visualize and model structures from chemical databases; build molecules and materials with interactive sketching, building, and editing tools; calculate and display key structural parameters; display the results of calculations as animated dynamics trajectories, graphs, and molecular models; annotate models for pictures and diagrams; and produce hardcopy output. Materials Visualizer runs under Windows 95, 98, or NT. Molecular Simulations 310 MathType is the professional version of the Microsoft Equation Editor. It is an interactive tool for Windows and Macintosh that lets users create mathematical notation for word processing and 48
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desktop publishing documents, Web pages, presentations, and TeX, LaTeX, and MathML documents. Users can quickly build complex equations with simple point-and-click techniques. MathType applies the rules of mathematical typesetting and automatically chooses fonts, style, spacing, and position as the user enters the equation. MathType comes with more than 275 mathematical symbols and templates. Design Science 311 MOE, the Molecular Operating Environment, a software system designed for molecular computing, integrates visualization, model building, simulation, and analysis of molecular structures. It includes a suite of ready-to-use applications for high-throughput-screening data analysis and combinatorial chemistry. MOE comes with source code for customization and an embedded programming language for prototyping and methods development. MOE is platform independent. Chemical Computing Group 312 NuGenesis SDMS enables scientists to unify, share, and reuse scientific data generated from the vast array of laboratory applications. NuGenesis Archive software provides a fast, reliable, and secure method for archiving and retrieving raw data within minutes of its creation or change. Using predetermined selection criteria, a database catalog is created automatically, and then the raw data are stored on safe, secure media (e.g., optical disks and zip drives). Raw data can be retrieved and restored with just a few mouse clicks. NuGenesis Unify software prints reports, including graphics, from any Windows-based application to the NuGenesis database and operates in batch or manual mode. NuGenesis Vision software is a mining tool to browse the database by sorting and filtering reports. Users can view reports from multiple analytical applications and can create compound documents. The software runs either in Windows 95 or NT environments. NuGenesis Technologies 313 PeakTrak software tracks samples and identifies peak fractions in chromatographic purifications. The program uses color-coded graphics to locate peak and nonpeak fractions in automated separations performed with Isco CombiFlash automated organic purification systems, ProTeam systems for protein purifications, and any system using an Isco Foxy 200 or Foxy Jr. fraction collector and detector with analog output. Key features and functions of PeakTrak software include on-screen color coding to identify each sample when performing unattended purifications of multiple samples;
labeling and color coding each peak with the fraction collector tube number that the peak is collected in; saving each chromatogram separately according to the sample ID entered either manually or with the barcode reader; annotating each data file with separation conditions, date and time, and other user-defined information; maintaining sample purification records for future reference; and saving chromatographic data in Microsoft Office-compatible format, making it easy to exchange data with most Windows-based software. Isco 314 pKalc estimates the acidity or basicity of compounds. Users enter structural formulas either graphically with a mouse or from the keyboard by means of an easily learned notation. From this information the program will calculate the pKa values, displaying the parameters of the calculations while they are in progress. pKalc is especially helpful for calculating pKa values when the experimental determination of pKa values is difficult or impossible. This situation occurs when the substance has a low water solubility or when the substance is unstable in water. The software can provide assistance with weak acids and bases, with unstable materials, and with insufficiently soluble substances. pKalc is compatible with Windows. CompuDrug 315 PSSWingPC is designed for use with gel-permeation and size-exclusion chromatography. It can process up to six detectors simultaneously and provides inter-
nal standard correction, chromatogram spreadsheet functions, and simultaneous integration with high-performance liquid chromatography results. Separate modules allow multi-instrument control, flow-driven data acquisition, and measurements for viscosity, light-scattering, chemical heterogeneity, and 2-D chromatography. The software is compatible with Windows. Polymer Standards Service 316 QikProp provides predictions for physically significant descriptors and pharmaceutically relevant properties important in determining ADME (adsorption, distribution, metabolism, and excretion) characteristics for drug candidates. Accurate predictions for as many as 10,000 compounds per hour can be made for cell permeabilty (two different scales), bloodbrain barrier permeability (log BB), central nervous system activity, polarizability, aqueous solubility (log S), octanol-water partition coefficient, and free energies of solvation in hexadecane, octanol, and wa-
ter. QikProp can be run under UNIX, Linux, and Windows (95, 98, and NT). Schrodinger 317 SHELXTL is a crystallographic software package that includes the programs needed for solving and refining routine and problem structures. It is capable of refining inorganic structures, minerals, organometallics, organics, and biological macromolecules such as natural products and proteins. The software is general for all space groups, numbers of atoms, and special positions. All space groups are handled automatically. The program sets up appropriate constraints for atoms in special positions and origin definitions in polar space groups. The space group is determined using information on symmetry, systematic absences, and intensity statistics. SHELXTL reads Protein Data Bank (PDB) files and prepares PDB files for deposition according to the latest guidelines. The software, which is derived from and compatible with SHELX, operates on a wide selection of hardware platforms. Bruker AXS 318 Substance Manager is integrated compound and plate management software that addresses critical bottlenecks in drug discovery programs generated in great part by high-throughput technologies. It supports the supply, management, and tracking of substances. Among the processes it performs are the following: It receives new vials or plates containing samples and assigns them to storage locations. It automates the plate preparation process, enabling compound management to prepare plates from vials, solubilize master plates, prepare replicate plates via robotics integration, and combine 96-well plates into 384- and 1,536-well plates. It enables scientists to search for substances and containers by substructure, exact structure or similarity, substance ID, bar code, container type, and location. The software runs on multiuser, multiplatform, multisite configurations. Emax 319 TOPKAT is a software-based system that computes and validates assessments of toxic and environmental effects of chemicals solely from molecular structure. It employs cross-validated quantitative structure-toxicity relationship (QSTR) models for assessing various measures of toxicity. The software comprises a user-friendly interface to guide users through a computer-based assessment of toxicity for a query structure and preconstructed QSTR models for assessment of rodent carcinogenicity, Ames mutagenicity, rat oral LD50, developmental toxicity potential, skin sensitization, fathead minnow LC50, Daphnia magna EC50, and
log P. The user enters a chemical structure and clicks on the effect of interest, and a computational assessment is generated. The software is compatible with Windows 95 and NT. Oxford Molecular 320 WinMASPHYC is a multipurpose molecular dynamics (MD) software package for Windows-based computers that allows users to build assemblies of molecules in a cell, to set up the calculations, and to interpret the results. Temperature- and pressure-controlled MD simulations can be done by employing the ParrinelloRahman and Nose methods. A velocity-
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scaling method can be used for controlled temperatures. Both the SHAKE algorithm and the rigid-body treatment can be applied to molecular systems. WinMASPHYC can be applied to systems such as organics, polymers, biomolecules, metals, ceramics, semiconductors, crystals, amorphous solids, liquids, and gases. Calculations for parameters such as phase transitions, expansion, compressibility, and tensile strength can be performed. Fujitsu
• Databases 321 Biotransformations is a stand-alone CD-ROM database that contains a subset of the Metabolism database and mirrors the "Biotransformation" seven-volume book series published by the Royal Society of Chemistry. The database comprises biotransformations of chemical entities, including pharmaceuticals, agrochemicals, food additives, and environmental and industrial chemicals in vertebrates within the animal kingdom, including mammals, birds, and fish. The CD-ROM runs under Microsoft Windows and in-
cludes all the chemical software required to phrase chemical queries and search the database. The database offers ready access to structural information on parent compounds and their metabolites within an intuitive Windows application. Query Wizard allows the user to quickly put together structure and text queries without the need to learn a complex query language. Keyword menus permit point-andclick access to the wealth of terms available for searching. Users can draw structure queries with their favorite chemical editor. Synopsys 322 ToxSys contains a wealth of toxicological information on more than 240,000 compounds and mixtures with exhaustive literature references, as well as a compendium of data on a variety of effects, such as toxicity, carcinogenicity, mutagenicity, and chronic effects. In addition, it contains an engine for computational analysis for prediction of toxic effects. A large endocrine disrupter subdatabase gives exhaustive results on a wide range of studies on the effects of these disrupters. ToxSys is a continuity product, with major new topics, subject areas, and analysis routines added semiannually in various areas of environmental health and science. It is designed to provide a wealth of information and easy-to-use analysis tools for a variety of professionals, including toxicologists; environmental and food scientists; health and safety regulators; medicinal, cosmetic, and fragrance chemists; and chemical safety professionals. SciVision
• CD-ROM or Online 323 Chem Sources-USA is a chemical buyer's guide that lists the product lines of hundreds of chemical suppliers throughout the U.S. and Canada. The Chemical Section (white pages) contains more than 155,000 chemicals arranged alphabetically by chemical name. CAS Registry Numbers are also given. The Trade Name Section (yellow pages) lists more than 7,000 trade name chemicals. The Company Section (blue pages) lists more than 900 chemical suppliers. Included are addresses and telecommunication information for each office. Chem Sources-International lists the product lines of thousands of chemical suppliers in more than 130 countries, including all information found in the U.S. directory. Chem Sources-Online allows users to find any chemical product and then offers options to pay for supplier information. Chemical Sources For information on numbered items, see Reader Service Card SEPTEMBER 25,2000 C&EN
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