Digital Briefs

Software

pCEL-X is software for simulation and refinement of permeability data from Caco-2, a drug transport model, and parallel artificial membrane permeability (PAMPA) determinations. The software uses nonlinear regression to tease out passive, paracellular, carrier-mediated, active-uptake, and efflux effects from pH-dependent data. It predicts permeability coefficients from a comprehensive internal database of Caco-2 and PAMPA measurements, Abraham descriptors, and structural information. The software is PC-based and is compatible with Windows. pION, www.pion-inc.com

(1) STN AnaVist v2.0 is an update of v1.1 with more data available for manipulation. The software works with STN (the online database service providing global access to published research, journal literature, patents, structures, sequences, properties, and other data) and CAplus (a database of more than 27 million patent and journal article references in hundreds of subject areas). This version includes the Derwent World Patents Index, a comprehensive database of more than 33 million patent documents. The product upgrades include new clustering fields, new bar-chart capabilities, over eight highlighting features to compare multiple data sets, and new 2-D displays. STN AnaVist v2.0 runs on Windows 2000 (SP3 or higher) and Windows XP. Chemical Abstracts Service, www.cas.org

ECCE (Extensible Computational Chemistry Environment) is application software that enables scientists to efficiently set up calculations and store, retrieve, and analyze the data produced by computational chemistry studies. The product provides a sophisticated graphical user interface, scientific visualization tools, and the underlying data management framework. Among its features are support for building molecular models, a graphical user interface to a broad range of electronic structure theory types and for basis set selection, and remote submission of calculations to UNIX and Linux workstations. ECCE runs on Linux, Sun, and SGI workstations. It is written in C++ using the X Window System Motif user-interface tool kit and OpenGL graphics. ECCE, www.ecce.emsl.pl.gov

(2) Conflex v5.2 searches the conformational space of a flexible molecule to find every optimal structure of chemically significant conformers. It contains features such as a conformation space search algorithm and a variable search limit. Conflex calculation results can be output in a variety of formats and can be used in applications for ab initio calculations or visualization applications. The product computes optimum geometry, conformations, and potential energy lists. New in v5.2, Conflex can calculate the energy using the generalized Born solvent model. Users can add the quasi-interaction effect to the force field. Users can also include additional constraints to specify the structural information. The software runs on Mac OS X 10.2 and higher, Red Hat Linux 7.1 and higher, and Windows XP. Conflex, www.conflex.us