Digital Briefs

Software

Collaborative Drug Discovery (CDD), a California-based firm, offers software to help scientists archive and organize all of their preclinical chemical and biological drug discovery data accumulated from both low- and high-throughput screens. Researchers can try to advance drug candidates more quickly by using the software's Web-based interface to selectively share data sets with other labs around the world and search collaborators' databases as well as a CDD public repository of results. The software allots each user group a private "vault" for securely storing experimental data in "the cloud"; groups additionally have the ability to grant access rights to specific collaborative partners. CDD's software package also includes tools for visualizing bioassay plate data and for searching by structure or substructure via ChemAxon's Marvin molecular visualization platform. In November 2008, CDD received a grant from the Bill & Melinda Gates Foundation for $1.8 million to further develop its database for accelerating the discovery of new therapies against tuberculosis. The firm hopes that this humanitarian project will generate a model for future work with industry and foundations targeting other neglected diseases. CDD, www.collaborativedrug.com

At the end of June, Thomson Reuters' Healthcare and Science businesses unveiled the firm's latest upgrade to its bibliographic management software, EndNote for Windows. In addition to working with Microsoft Word and Apple Pages '09, the new version, EndNote X3, now also enables users to insert references in more than 3,700 journals' styles into their manuscripts while writing in the program OpenOffice.org Writer. Designed with chemists in mind, the software additionally allows users to create multiple bibliographies within a document (as might be necessary in a book or graduate student thesis) and to group citations by number and letter and then cite just a portion of a specific group, a common practice in chemistry journals. Scientists can also use EndNote Web features to keep track of personal citation metrics: They can organize publication lists in ResearcherID, a free online author community that links to details about the number of times they've been cited on ISI Web of Science. Thomson Reuters, www.endnote.com

Launched in July, JChem for Excel is the latest addition to the JChem-Marvin software suite developed by cheminformatics firm ChemAxon. This new add-in combines the structure management and search capabilities of JChem with the molecular visualization and drawing attributes of Marvin and integrates them into the Microsoft Excel spreadsheet environment. Users can add "live" structures to spreadsheet cells and then perform structure-based predictions on them. The results of these calculations, such as pK_a values and atomic charges, are stored in the spreadsheet cells and automatically updated when structural edits are made. JChem for Excel also supports R-group decomposition during searches: A central scaffold for a molecule is generated and ligands at certain attachment points can be queried. ChemAxon promises to integrate even more functionality from its other software into future versions of this new product. ChemAxon, www.chemaxon.com

Released in July by Cranbury, N.J.-based Millsian Inc., Millsian v2.0 Beta is a 3-D molecular visualization program that can calculate the physical characteristics of structures of almost any size or complexity. Chemists can use the software to build structures or import them from databases; it handles and converts between SMILES, MOL, and PDB file formats. Large imported structures such as those of proteins or DNA fragments (shown) can be edited and corrected for missing hydrogens or miscalculated bond orders. Users can further evaluate binding pockets and reactive sites in structures with the help of analytically calculated whole-molecule charge distribution profiles. In addition, they can compute dipole moments and rotational barriers for molecular conformation changes. To download a free trial version of the software, visit the company's website. Millsian Inc., www.millsian.com

Website

Wolfram Alpha is a free online "computational knowledge engine" based on Wolfram Research's Mathematica technology. Launched in May, Wolfram Alpha contains terabytes of factual data covering a wide range of fields, including chemistry, and 6 million lines of Mathematica code for answering queries. For instance, a chemist could type "500 mg of silver nitrate," and the knowledge engine would return "2.94 mmol," as well as a variety of other information, including the thermodynamic properties of that specific quantity of the compound. The Web-based engine's aim is "to collect and curate all objective data and make it possible to compute whatever can be computed about anything," according to the company. Wolfram Alpha, www.wolfram alpha.com