Digital Briefs

The following products were on display at the exposition during the American Chemical Society's national meeting in Atlanta.

Software

Molecular Operating Environment (MOE) is a comprehensive suite of computational chemistry, molecular modeling, and informatics software. Its individual applications include Protein Modeling, Structure-Based Design, Bioinformatics, Molecular Modeling and Simulations, and Methodology Development and Deployment. MOE is portable and allows users to run the software on a wide range of hardware and platforms, including Windows, Linux, Mac OS X, and various UNIX versions. Chemical Computing Group, www.chemcomp.com

Meteor is expert-knowledge-based software for predicting the metabolic fate of chemicals. The researcher provides a chemical structure, and the software predicts the most likely first generation of metabolites, taking lipophilicity, structural features, and competing biotransformations into account. Each metabolite is subsequently analyzed to predict further metabolism. Meteor then displays the tree of metabolites with supporting data. If the scientist inputs the masses of the metabolites identified by mass spectrometry along with the molecular structure of the parent compound, Meteor can also predict the chemical structures of the metabolites. The software is compatible with Windows. Lhasa, www.lhasalimited.org

CombiGlide is a structure-based virtual screening program for the design of optimal, focused combinatorial libraries. Combinatorial chemistry and parallel synthesis techniques can generate far more compounds than can be practically synthesized or screened. This software helps create smaller libraries that exhibit druglike physiochemical properties and are biased toward a specific target or class of targets. CombiGlide's high-throughput docking methodology accurately estimates ligand-binding affinities, identifies potent members of a virtual library, and eliminates unpromising compounds. The software supports Linux and SGI. Schrödinger, www.schrodinger.com

ADMET Predictor 1.2.3 predicts the most important properties related to oral absorption, as well as several pharmacokinetic properties and many aspects of toxicity: pK_a, human effective permeability, native solubility in pure water at 25 ^oC, native pH at saturation in pure water, salt solubility factor, log P, log D, and others. Besides providing estimates of critical adsorption, distribution, metabolism, excretion, and toxicity properties for single compounds, ADMET Predictor can be used for high-throughput in silico screening of large compound libraries. The software is designed to run on Windows. Simulations Plus, www.simulations-plus.com

Un-Scan-It V 6.0 automatically extracts x,y values from hard-copy graphs. The software works with any scanner or digital camera to extract data values from strip charts, recorder output, published graphs, HPLC traces, or any other graphical image. It includes features for integrating peak areas, removing grid lines, rescaling graphs, smoothing data, taking derivatives, and fitting curves. The data can be saved in ASCII or clipboard format and imported into most spreadsheet and graphics analysis programs. The software is available for Windows and Macintosh. Silk Scientific, www.silkscientific.com

Orbdraw is a visualization program for displaying molecular orbital and electron density data from Gaussian, Gamess, Jaguar, Hondo, Mopac, or Ampac calculations. Orbdraw can display the molecular orbitals, electron densities, or spin densities in 3-D as either wire frames or solid surfaces and can map orbitals or charges onto the density surfaces. The images can be rotated about any axis. The user can select the orbital to display, the resolution, the threshold value, and the type of display. The orbitals are displayed over the molecular structure, and the structure can be displayed either as a stick figure or with tubular bonds. The graphics images can be saved in several different graphics formats. The software is available for Windows, Macintosh, and Linux. Serena Software, www.serenasoft.com

CrystalMaker 7.1 for Mac OS X is now available as a universal binary, which is an executable file that runs on both PowerPC- and Intel-based Macs. CrystalMaker is a program for building, displaying, and manipulating all kinds of crystal and molecular structures with real-time photorealistic graphics and 3-D viewing. It allows scientists to accentuate the three-dimensionality of structures by fading out more distant atoms (depth fading). A new feature is the ability to control the opacity of foreground atoms. These atoms can be made transparent; more distant atoms gradually become visible, while the most distant atoms fade into the background again. In this way, scientists can look "inside" a dense, complicated structure with the option of profiling different depths in the material. CrystalMaker Software, www.crystalmaker.com

ACD/IntelliXtract extracts all liquid chromatography and mass spectrometry components in a data set and identifies the molecular ions, isotopic ions contributing to each ion cluster, primary adduct ions, primary neutral losses from the molecular ion, primary fragment ions, and multimers. The software determines the accurate retention time for each eluting chromatographic peak for all masses in the data set. It determines which eluting ions in a retention time region combine to form a single eluting component. It evaluates the quality of the data on the basis of the expected ¹²C to ¹³C ratio. ACD/IntelliXtract supports LC/MS data from all major instrument models. Advanced Chemistry Development, www.acdlabs.com

AFITT, a graphical tool for building macromolecules, was developed to help protein crystallographers create virtual molecules and to promote better communication between chemists and crystallographers. It allows energetically reasonable ligand conformers to be generated from SMILES codes and provides easy access to crystallographic structure refinement via dictionary generation. It includes real-time and real-space fitting with the Merck molecular force field and electron-density shape. It permits linking to structural and chemical corporate databases. AFITT works on all common platforms. OpenEye, www.eyesopen.com

SYBYL 7.2 is a suite of computational informatics software designed to enhance the drug discovery workflows and decision-making of computational chemists and molecular modelers. It includes comprehensive tools for structure building, optimization, and comparison; visualization of large and small molecules and associated data; annotation, hard-copy, and screen-capture capabilities; and a wide range of force fields. The software is compatible with SGI, IRIX, and Linux. Tripos, www.tripos.com

ToxBoxes 1.1 provides predictions for three basic toxicity endpoints: acute toxicity, genotoxicity, and organ-specific health effects. The software uses large and validated databases and robust structure-activity relationship models in combination with expert knowledge in organic chemistry and toxicology. It allows users to check the availability and behavior of compounds. It identifies and displays toxicophores. It includes a reference compound dictionary of marketed chemicals and drugs. The software is compatible with Windows, Mac, Linux, and UNIX. Pharma Algorithms, www.ap-algorithms.com

CD-ROMs

The Joy of Toys is a CD containing toy-related chemistry resources from the Journal of Chemical Education. It includes activities, demonstrations, experiments, and informational articles, along with video clips from the Chemistry Comes Alive! series. The index can be searched by keywords correlated to the science standard content area, by a specific type of toy, and by type of curriculum item such as demonstration or experiment. JCE, www.jce.divched.org

Databases

FamPat contains nearly 40 million records from more than 75 worldwide patenting authorities. It merges patent information from the European Patent Office, the U.S. Patent & Trademark Office, the World Intellectual Property Organization, the Japan Patent Office, and others. It is updated with technologies from major countries within one to two weeks of patent office publication and contains English-language abstracts. FamPat Plus is a full-text, key-content enhancement to FamPat. Questel Orbit, www.questel.orbit.com

Genetox is a database of chemical and toxicity data from the Food & Drug Administration's Center for Drug Evaluation & Research. It covers 231 drugs and drug products with 4,414 toxicity tests. It includes genetic toxicity information extracted from pharmacological reviews contained in New Drug Approvals. Some of the toxicity endpoints described are bacterial and mammalian mutagenesis tests, chromosome aberration tests, and micronucleus tests. Leadscope, www.leadscope.com

Online

SpectroscopyNOW.com is a free resource for all spectroscopists. It covers atomic, infrared, mass, Raman, NMR, ultraviolet, and X-ray spectrometry, as well as magnetic resonance imaging, chemometrics, and proteomics. The site offers news, features, a directory of links, e-zines, books, a list of conferences, databases, a training center, opinion polls, and classified ads. John Wiley & Sons, www.spectroscopynow.com

Pharmaceutical Substances is a structure-searchable online reference that provides a compendium of more than 2,400 active pharmaceutical ingredients of interest to the chemical and pharmaceutical industries. Information is collected from the relevant literature and commercial patent data. It includes synthetic routes and intermediates for newly approved drugs. It is updated biannually. Thieme, www.thieme-chemistry.com

MCWeb is a Web application that can predict various toxicological endpoints on the basis of structural fragments. It assumes that the presence of molecular fragments previously found in active compounds is indicative of potential activity. MCWeb gives an estimate of the probability of toxic activity for almost any organic molecule entered with KLN or SMILES codes, normal chemical structure input, or computer graphics. It also provides an explanation of how the conclusions were reached. The application predicts water solubility, octanol-water partition coefficients, human intestinal absorption, and rat LD₅₀ values. MultiCase, www.multicase.com