Digital Briefs

Software

PETRA (parameter estimation for the treatment of reactivity applications) is software for the rapid calculation of physicochemical effects in molecules. It can be applied to pharmaceutical lead discovery and lead optimization, definition of similarity and diversity of combinatorial libraries, quantitative structure-activity and structure-property relationship projects, and prediction of spectra and chemical reactivity. The software comprises methods for calculation of electronic and energy effects in organic molecules. It handles high volumes of structures such as those in company databases and combinatorial chemistry experiments. PETRA is available for most UNIX workstations. Molecular Networks, http://www.mol-net.de

ZDOCK and RDOCK are computational methods that establish the important geometric relationships and predict the manner in which two proteins interact at the atomic level. The rigid-body docking program, ZDOCK, uses a fast Fourier trans form to search all possible binding modes for proteins of inter est, evaluating based on shape complementarity, desolvation energy, and electrostatics. The top 2,000 predictions are then given to the refinement program, RDOCK, where they are minimized by CHARMM to improve the energies and eliminate clashes, and then the electrostatic and desolvation energies are recomputed by RDOCK. The software runs on Linux, Mac, and several UNIX platforms. Accelrys, http://www.accelrys.com

ACD/PhysChem 8.0 makes it possible to predict the entire range of required physicochemical properties, including log P, pK_a, aqueous solubility, log D, and polar surface area, for hundreds of compounds per minute. The software applies leading algorithms to large databases with tens of thousands of compounds at a time, allowing the rapid and automatic screening of compound libraries. New to this version is ACD/pKa Accuracy Extender, which enables chemists to train the system with their own experimental data in order to calculate more accurate pK_a values for novel chemical classes. The software is available for PC- and UNIX-based systems. Advanced Chemistry Development, http://www.acdlabs.com

Databases

Structural Database of Allergenic Proteins (SDAP) is a Web server that integrates a database of allergenic proteins with various bioinformatics tools for performing structural studies related to allergens and characterization of their epitopes. The database includes more than 700 allergens and isoallergens and more than 800 protein sequences. Computational tools include the ability to search a protein against all SDAP allergens, to search an epitope (peptide) for exact matches in all SDAP allergens, and to search an epitope for similar regions in all SDAP allergens. Also included are links to protein databases, protein classification websites, and bioinformatics servers. http://129.109.59.107/SDAP

Biopendium enables researchers to identify potential drug targets, investigate close and distant relatives, and select corresponding proteins in experimental model systems. Relevant 3-D protein structures and ligand-drug interactions are available and include data relevant to approximately 80% of known drug targets. Comprehensive coverage of more than 150 complete genomes, including human, mouse, and rat, is a strong feature. Visualization and interpretation tools include an interactive alignment editor, exclusive ligand interaction viewer, and 3-D structure viewer. MDL, http://www.mdl.com

Online

SeparationsNOW.com is a free-access website for anyone working with separations technologies such as high-pressure liquid chromatography, gas chromatography, electrophoresis, hyphenated techniques, and ion chromatography, as well as those doing research in proteomics and genomics. Each technology has its own page with the latest news, features, jobs, links, and special offers on books. Monthly e-mail newsletters are also available. http://www.separationsnow.com

Current Protocols Online provides scientists with the latest information and methodologies for experimentation in their areas of research, including nucleic acid chemistry, pharmacology, protein science, and toxicology. The new version greatly expands both search and browse capabilities. The improved Fielded Search Function enables users to restrict a search to unit and protocol titles to go directly to the desired laboratory method and to search all of the text or to search content by DOI. PDF File Access allows users to print a PDF file of any Current Protocols Online unit, including all figures and tables. Wiley InterScience, http://www.mrw.interscience.wiley.com/cp

Martindale's The Reference Desk is a website that has literally thousands of links to websites of interest to scientists in their work and in their lives. It is divided into categories such as Chemistry Center, Language Center, Computers/Internet, Education, Electronic Media, Entertainment & Arts, International Travel, International Business, Science Tables, and Astronomy/Space Center, to name a few. For example, the Calculators Online section has links to more than 18,000 calculators. http://www.martindalecenter.com

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