DS Modeling 1.1, Tarari, Biopython 1.2, Cytoscape, MageBuilder, PDIsorder v 1.0

Accelrys last week released DS Modeling 1.1, an application for its Discovery Studio product family. DS Modeling 1.1 is a client-server environment for in silico modeling and simulation research on Windows-based PCs. Available components include DS HT-Xpipe for structure determination of protein-ligand complexes; DS Xbuild for fitting protein structures into electron density maps; DS Xligand for ligand-fitting in electron density maps; DS CNX X-ray for structure refinement, map calculation, water placement, and structure validation using experimental X-ray data; DS GeneAtlas for identifying biochemical function from protein sequences; and DS AtlasStore — a proteomic database that incorporates data-mining and visualization of functional annotation data from genomic data.

IT acceleration firm Tarari has launched the Tarari High Performance Content Processor, which offloads compute-intensive algorithms from servers, cluster nodes, and embedded processors to increase the available cycles in clustered computing applications as well as individual servers and processors. According to the company, the processor has applications in a variety of fields, including genomic research, pharmaceutical research, and molecular modeling.

Biopython 1.2 is available at http://www.biopython.org/download/. The release includes a EUtils library for accessing databases at NCBI, a gene expression analysis package, and a PDB package.

The Computational Biology Center at Memorial Sloan-Kettering Cancer Center has released a plug-in for the Cytoscape visualization tool to read the Proteomics Standards Initiative-Molecular Interactions (PSI-MI) format at http://www.cytoscape.org/plugins.html.

MageBuilder, a tool for converting tabular data into MAGE-OM objects, is available at http://cybertory.org/software/MageBuilder/MageBuilder_ index.html.

PDIsorder v 1.0, a program for predicting ordered and disordered regions in protein sequences, is available from Softberry at http://www.softberry.com/berry.phtml ?topic=pdisorder&group=programs& subgroup=propt.