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Environment

Digital Briefs

New Software And Websites For The Chemical Enterprise

by Janet S. Dodd
December 19, 2005 | APPEARED IN VOLUME 83, ISSUE 51

Software

Maestro, the unified interface for all Schrdinger software, has an array of features for various functions. High-resolution, presentation-quality images can be incorporated into documents for publication or for sharing data with colleagues. For model generation, Maestro supports many common file formats for structural input and provides an intuitive, full-featured building tool for constructing molecular models of any type. Multiple viewing options accommodate the varied needs of different applications. For quantitative structural analysis, versatile measurement tools give the user the ability to quantify a molecule's structural features. Superimposition tools make possible detailed comparisons between structures. Maestro offers the ability to customize and automate tasks via scripting in the Python language. The latest version of Maestro, version 7.5, is free to all academic users. Schrdinger, www.schrodinger.com

ACD/Ion Presence is software for processing, analyzing, and managing mass spectrometric data. Users can automatically find and label LC/MS peaks with a specified mass and identify and label peaks with a user-specified difference from a reference mass value. This feature is useful for targeting the peaks for a parent drug and searching for expected metabolite transformations, for finding expected impurities, or for quickly identifying the targeted compound in high-throughput purity analysis. This automatic labeling feature can be applied to the extracted data at any time during data review without the need to perform data reprocessing. The software is available for Windows. Advanced Chemistry Development, www.acdlabs.com

MDL Notebook is an electronic laboratory notebook system that combines the flexibility and proof-of-invention legality of paper notebooks with the robust data-handling capabilities of electronic systems. Tasks are streamlined, routine reaction setup calculations are automated, and experiment details are securely stored in Oracle. Data can be quickly stored, searched, and reused. When the experiment is complete, a hard-copy report is produced to satisfy intellectual property requirements. The software is compatible with Windows. Elsevier MDL, www.mdl.com

Mobius 2.0 Candidate Design Environment allows researchers to identify drug candidates by combining computational and medicinal chemistry resources. Users select computational tools that are relevant to their project and assign priorities to the criteria evaluated by these tools. Mobius then finds possible structures and uses the selected computational tools to evaluate them, generating data about the predicted performance of each structure. Mobius is an interactive desktop-based environment that can be installed on a PC running either Windows or Linux attached to a multiserver system. Coalesix, www.coalesix.com

Mercury is software for structure visualization and exploration of crystal packing. It has a full range of structure display styles as well as the ability to measure and show distances, angles, and torsion angles. It creates and displays centroids, least-squares mean planes, and Miller planes. It can display unit cell axes, the contents of any number of unit cells in any direction, or a slice through a crystal in any direction. It provides the location of intermolecular and intramolecular hydrogen bonds, short nonbonded contacts, and user-specified types of contacts. It has the ability to build and visualize a network of intermolecular contacts and to show extra information about the structure, such as the chemical diagram and atomic coordinates. Users can calculate, display, and save powder diffraction patterns. It is available as a free download or as part of the Cambridge Structural Database system for Windows, Linux, and UNIX platforms. Cambridge Crystallographic Data Centre, www.ccdc.cam.ac.uk

Databases

TOXNET (toxicology data network) is a group of 13 databases covering toxicology, hazardous chemicals, environmental health, and related areas. Some examples are as follows: The Hazardous Substances Data Bank focuses on the toxicology of potentially hazardous chemicals; the Integrated Risk Information System contains carcinogenic and noncarcinogenic health risk information; Tox Town is an interactive guide to commonly encountered toxic substances; Haz-Map links jobs and hazardous tasks with occupational diseases and their symptoms; and TOXMAP uses maps of the U.S. to show the amount and location of toxic chemicals released into the environment. National Library of Medicine, www.toxnet.nlm.nih.gov

Online

Connotea is a free online reference management service for scientists. It allows users to store their Web links online so they can be accessed from any Web browser. Web links can be organized with individually chosen tags. The site also allows users to share their links with others and discover links to new publications or other resources relevant to their interests. Users can bookmark a paper by simply highlighting its DOI in their browsers or by entering the DOI of a paper. They can share this bookmark with everyone or privately within a group. Nature Publishing Group, http://www.connotea.org

Podcasts

Podcasts are audio and video programs accessed on the Web. They can be played on any computer with audio-playing software or on a digital audio player. By downloading a free program, called an aggregator, and subscribing to a publisher's site, users can automatically receive new content as soon as it is made available. Some podcasts of interest to chemists are as follows:

Nature: www.nature.com/nature/podcast

This Week in Science (TWIS): www.twis.org/TWIS-science-podcast.html

Science Friday: www.sciencefriday.com/audio

Science@NASA: science.nasa.gov


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

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