Digital Briefs | April 26, 2004 Issue - Vol. 82 Issue 17 | Chemical & Engineering News
Volume 82 Issue 17 | pp. 29-31
Issue Date: April 26, 2004

Digital Briefs

New Software And Websites For The Chemical Enterprise
Department: Science & Technology
MolWorks 2.0
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MolWorks 2.0

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

Software


MolWorks 2.0 is an integrated program for chemical, biological, and materials research that enables scientists to aggregate many computational chemistry programs. MolWorks sets up the details of molecular orbital calculations for many external programs, such as Gaussian, Q-Chem, and Gamess. The user can execute these calculations on a local laptop and on remote servers. The software is compatible with Windows, Mac OS X, and Linux. Best Systems, http://www.bestsystems.co.jp

LigPrep
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LigPrep

HyperChem 7.5 is a molecular modeling environment that unites 3-D visualization and animation with quantum chemical calculations, molecular mechanics, and dynamics. Version 7.5 introduces the OpenGL model, which gives a generally higher quality of graphics and provides enhancements to protein modeling and visualization. Secondary structures extracted from Protein Data Bank files can be rendered using a variety of cylinders, ribbons, and coils to characterize complex topographies. Any atom can be individually rendered. Electron densities for large proteins can be rapidly computed. The software is Windows compatible. Hypercube, http://www.hyper.com

Molecular Conceptor 2
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Molecular Conceptor 2

LigPrep is software for preparing high-quality 3-D molecular models of druglike molecules from 2-D or 3-D structures to enable property prediction or 3-D modeling, such as docking or ligand-based drug design. LigPrep can add hydrogen atoms to produce all-atom structures, can remove counterions that are often present in database structures and cause problems in processing, and can neutralize functional groups by adding or removing hydrogen ions to accommodate programs that prefer neutral species. The software can generate ring conformations and stereoisomers consistent with specified stereochemical information. LigPrep runs on UNIX and Linux platforms. Schrödinger, http://www.schrodinger.com

ACD/ChemSketch 8.0
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ACD/ChemSketch 8.0

InforSense 1.9: ChemScience is a software application module for streamlining chemistry research within the InforSense Knowledge Discovery Environment (KDE). This application enables chemists to build a range of cheminformatics processes, from analysis and visualization of chemical libraries to quantitative structure-activity relationships and molecular modeling. The software enables researchers to handle all the steps from data generation through analysis, simulation, and reporting. InforSense, http://www.inforsense.com

CrystalMaker 6.3
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CrystalMaker 6.3

Molecular Conceptor 2 is a multimedia courseware package that teaches principles and concepts of drug design and molecular modeling. Version 2 offers a Presentation Mode, which includes a resizable window and a My Notes window in which users can insert comments on each page. It also includes reference support with an option to view the article, related Web links, related Molecular Conceptor page links, media description and source (Protein Data Base Reference Access), and author information. Users can get automatic live updates by clicking on the toolbar. Synergix, http://www.molecular-conceptor.com

STN Express with Discover! Analysis Edition (V 7.0)
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STN Express with Discover! Analysis Edition (V 7.0)

Science Direct is an electronic collection of science, technology, and medicine full-text and bibliographic information. It provides access to abstracts, references, and full-text articles in more than 1,800 peer-reviewed journals and is fully searchable. It is available by institutional subscription, but parts of the service are open to nonsubscribers, for example, viewing tables of contents and abstracts and purchasing full-text articles. http://www.sciencedirect.com

ACD/ChemSketch 8.0 is a chemical drawing package that enables users to draw molecules, reactions, and schematic diagrams; calculate physical properties; generate accurate IUPAC names for chemical structures; and design professional reports and presentations. With the addition of new bond types and molecular classes, Version 8.0 extends its capabilities to inorganic chemicals and polymers. Bond types include delocalized, aromatic, and quadruple bonds. Users can now construct organometallics and other coordination compounds. Advanced Chemistry Development, http://www.acdlabs.com

CrystalMaker 6.3 is a program for building, displaying, and manipulating all kinds of crystal and molecular structures with real-time photo-realistic graphics and 3-D viewing. The program features support for data input and output with autodetection and loading of major database formats as well as a range of data export options. Massive cluster visualization is possible with interactive editing of molecular structures to create crystal surfaces and defects or to import a molecule into an existing structure. The software was designed for the UNIX-based Mac OS X operating system. CrystalMaker Software, http://www.crystalmaker.com

Reactor performs chemical transformations and allows users to build a library of reactions that can be applied for any compounds having the same functional group. The software features a standard reaction format, simple atom-mapping methods, stereo-specific processing, a reaction site recognition engine, and reverse reaction processing. This Java-based program runs across many operating systems. ChemAxon, http://www.chemaxon.com

STN Express with Discover! Analysis Edition (V 7.0) helps information professionals search and retrieve information from scientific and technical literature and patents. The new 2-D Analyze Wizard easily analyzes and tabulates data and automatically creates charts and graphs in Excel. This version introduces tools for chemical structure analysis and assistance in query development with the CA Lexicon. Also, the Variable Group Analysis Table identifies the common substructure for an answer set of substances identified in the CAS Registry. Chemical Abstracts Services, http://www.cas.org

TranSiesta-C is capable of first-principles modeling of the electrical properties of nanoscale devices coupled with metallic electrodes. It combines Nonequilibrium Greens function techniques with density functional theory for electronic structure calculations. The software is also accurate for structural optimization of molecular and bulk systems. Atomistix, http://www.atomistix.com

BioMedCAChe 6.1 has structure-guided drug design and protein analysis tools that make it easy to set up and run automated docking experiments for whole libraries of ligands and drug candidates on a Windows computer. The ActiveSite option with the new FastDock automatic ligand docking docks flexible or rigid ligands into proteins with flexible or rigid side chains, using a Lamarckian Genetic algorithm and Potential of Mean Force (PMF) scoring with patent-applied-for enhancements. Solvation and entropy are handled implicitly. CAChe Group, Fujitsu, http://www.cachesoftware.com

Lucia drug discovery software provides a comprehensive overview of published and patented information about drug targets and antitargets. The presentation of the structural data makes it easy to group known inhibitors in scaffold groups and lay out a project plan around patentable chemotypes. In the lead discovery and optimization phase, Lucia helps prioritize compounds for synthesis or purchase based on their predicted properties. The eScreen modules for potency and selectivity are specific for a target or gene family. The program is Web-based and requires only a Web browser and the ChimePro plug-in. Sertanty, http://www.sertanty.com

Credit: BioMedCAChe 6.1
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Credit: BioMedCAChe 6.1
Credit: ADRIANA
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Credit: ADRIANA

ADRIANA (Automated Drug Research by Interactive Application of Nonlinear Algorithms) is a set of drug design and discovery tools combined under a graphical user interface. It can be applied to hit identification and lead finding, classification and prediction of biological activity and physicochemical properties, virtual screening of compound collections, and selection of molecular descriptors. It features automatic 3-D structure generation, empirical methods for calculation of quantitative descriptors, and calculation of molecular surfaces and surface properties. The software is available for UNIX workstations. Molecular Networks, http://www.mol-net.de

Cabinet is a network that contains more than a dozen interacting servers, for example, the World Drug Index (WDI), Planet, Empath, and QSAR. WDI is a database of drugs and trial preparations. It includes structures, enzyme functionality, and pharmacology. Planet is database of protein-ligand interactions with interaction diagrams that provide a 2-D synopsis of hydrogen bonding, van der Waals interactions, and solvent accessibility. Empath is a reference for biochemical processes in different organisms, providing pathway discovery mechanisms. QSAR includes more than 18,000 structure-activity relationships. Metaphorics, http://cabinet.metaphorics.com

Pipeline Pilot 4.0 is a high-throughput data analysis and mining system for drug discovery informatics. With this package, a user can define and perform a complex series of operations on extremely large data sets in real time. The new release includes a browser for simplified integration with external Web services, an upgraded driver for faster database access, and new Java and Perl libraries for easier component development and integration with third-party tools. In addition, enhancements to the data representation facilitate the creation of applications in areas like bioinformatics and report generation. Scitegic, http://www.scitegic.com

ClassPharmer Suite 3.2 is designed to be used by computational chemists and medicinal chemists for rapid and in-depth analysis of data from screening. It provides an automated mechanism for learning structure-based classes from primary, secondary, or even virtual screening data that can be used in a variety of applications. These classes organize the compound space and reduce the effects of noise in the data. Users can get additional insight by adding other tested compounds to the learned classes based upon scaffold similarity and by importing or calculating additional class and compound attributes. Evidence for decisions at various stages in the discovery process can be retrieved, reviewed, revisited, or reworked at any time. Bioreason, http://www.bioreason.com

Credit: VirtualLab
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Credit: VirtualLab

VirtualLab is an integrated informatics platform for workflow automation, instrument integration, and electronic laboratory notebook functionality. The software facilitates experimental design, execution, and analysis in a way very similar to a researcher's natural manner of working. Common information need only be entered once, complex unit conversions are performed automatically, and design parameters are easily applied to generate multiple experiments. VirtualLab then collects and integrates process and analytical data from multiple lab instruments as well as from traditional bench chemistry activities. The resulting data are presented for analysis in a user-friendly manner and stored in a structured, portable, and searchable format. These activities are all performed within a secure environment and support compliance with 21 CFR Part 11 and other regulatory requirements. Mettler Toledo AutoChem, http://www.mtautochem.com

 

Online


ChemGuide and MedPharmGuide are search engines for chemistry or medicine and pharmacology information on the Internet. They cover only individually selected topic-related servers for retrieval of relevant information with few off-topic hits. PublishersGuide is a search engine covering the Web servers of publishers, institutions, and societies that publish in science and technology. Fiz Chemie Berlin, http://www.fiz-chemie.de

STUDENTS AND TEACHERS


NetTutor V 5.1 is a distance-learning environment for the dissemination of online content. This Web-based graphical chat room allows students to use their own computers to access learning materials in a nonlinear fashion or in real time with live tutors. The administration portion enables teachers to place students into groups and then organize and control the groups. Teachers can create assignments using an interactive whiteboard to render mathematical and scientific notation. The program requires Netscape or Internet Explorer. Link Systems, http://www.link-systems.com

Odyssey is a suite of instructional software for introductory chemistry classes in high schools, colleges, and universities. Separate editions are available for students, for instructors, and for the laboratory. Featuring an integrated molecular dynamics simulation engine, the software provides a highly interactive environment with more than 70 fully developed activities covering a variety of fundamental chemistry topics. Molecular simulations are carried out in real time by a fully integrated computational engine. In addition to more than 200 pages of chemistry content, Odyssey includes a collection of student-assignable worksheets and an extensive, annotated library of molecular models. The software is compatible with Windows. Wavefunction, http://www.wavefun.com

ChemIST is a CD for students designed to complement introductory textbooks. Highly interactive, it features video clips and animations of chemical reactions at both macroscopic and microscopic scales. Also, 3-D molecular models can be grabbed with the mouse and rotated to see all perspectives. Every topic has a set of follow-up questions that allow students to assess their understanding of the material. The product requires Internet Explorer or Netscape. Prentice Hall/Pearson, http://vig.prenhall.com

ChemCollective is a website resource for introductory chemistry educators in high schools and colleges who are looking for techniques to help their students approach chemistry more like practicing scientists and see interesting real-world applications of key concepts. The bulk of the site centers on the Virtual Lab, which is a networked laboratory simulation, and the scenario-based learning activities developed by faculty at Carnegie Mellon University. http://www.chemcollective.org

WebAssign features a ready-to-use database of textbook questions, instant grading with weighted categories and scores, maximum accessibility, and technical support for teachers. The textbook questions are taken directly from popular textbooks, and teachers can write their own questions and edit existing ones. Questions can be multiple choice, true/false, matching, fill in the blank, short answer, rank order, numerical, essay, or file upload. Assignments are accessible from any Web connection at all times. For students, forums, bulletin boards, simulations, animations, and chemical drawing tools are available. http://www.webassign.net

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

 
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