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Downloads and Upgrades: Nov 5, 2010

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The Chemical Computing Group has released PSILO version 2010.09 – a protein structure database system that allows for an integrated repository of proprietary and non-proprietary structural data. The system lets researchers register, annotate, track, and share experimental and computational macromolecular structural data and provides bioinformatics and cheminformatics searches with analysis and visualization capabilities through a standard web browser interface.

According to the developers, the latest version of the tool lets users perform 3D searches for protein-ligand and protein-protein interactions by querying structural data directly from standard sketchers. It also facilitates searches for common contacts and other motifs in the protein structure database and offers faster pocket similarity searching.

In addition, the system can now automatically perform annotations for all deposited structures including assignment of domain identifiers, Gene Ontology terms, SCOP classes, antibody CDR regions, kinase domain regions, and Blast neighbors, the company said.


SAS has released JMP Genomics version 5.

This version of the tool lets users organize analysis results into tabbed reports and customize the display of analysis options. It also includes a wizard that walks users through the import and analysis of new data sets; and supports integration with the R open-source statistical programming language, Microsoft Excel and other tools. The tool also lets users create custom add-ins to enhance the capabilities of JMP and share within their organizations or with other groups.

Other features include import support for SAM files and new track types, such as histograms and heat plots, tools for analyzing and viewing summaries of next-gen data from various technologies, support for rare variant summarization and analysis, and new capabilities for allele-specific expression analysis.

Version 5 also features a new Q-K Workflow that streamlines association analysis and simultaneously corrects for population structure and sample relatedness, screens for interactions between pairs of SNPs or test associations between SNPs and multiple traits simultaneously, and allows estimation of linkage disequilibrium blocks for calculating haplotype frequencies within blocks.

Finally, the software includes a "Get IPA Pathways" function that allows users of JMP Genomics to upload their gene lists to Ingenuity Pathways Analysis and add IPA pathway information to analysis datasets for gene set enrichment tests. It also includes tools to summarize individual expression deviations to identify significantly affected pathways.


This week, Reactome announced that it has released a new web interface for its open-source curated database of pathways and reactions.

Included in this release are a new suite of data analysis tools; an SBGN-based visualization system of pathway diagrams with advanced navigation features, including zooming, scrolling and event highlighting; and PSIQUIC web services to overlay pathway diagrams with molecular interaction data from the Reactome functional interaction network and external interaction databases.

Also included are pathway and expression analysis tools, which allow researchers to analyze experimental datasets by providing ID mapping, pathway assignment and over-representation analysis, a plugin for Cytoscape, improved tools for display and analysis of Ensembl Compara ortholog-based pathway predictions, and a species comparison tool, which allow users to compare pathways from other species with human data.


The European Bioinformatics Institute this week released the first public version of easyDAS — a web application that’s used to automatically create distributed annotation system sources hosted at the EBI.


This week, Affymetrix announced the beta release of the next version of its Fusion Software Developers Kit.

The beta includes C++ and Java source code, file format documentation, and libraries in support of the new CDF file format that the company plans to implement by the end of this year.

According to the developers, the current version of the Fusion SDK, version 1.1.0, must be installed prior to installing the new beta release.

The current full Fusion SDK and the beta package are available here.


R.E.D. Server 2.0 is now available. The web service is designed to automatically derive RESP and ESP charges, and to build force field libraries for new molecules and molecular fragments.

This version of the tool has various approaches for atom reordering; includes RESP and ESP charge derivation for whole molecules and molecular fragments; lets users build force field libraries for whole molecules and potentially for any type of molecular fragments; contains highly reproducible charge values independently of the QM programs or initial structures selected; includes the reinforcement of charge reproducibility; and has a statistic module that allows charge value comparisons among other features.

The server runs on a cluster of quadri-core Intel Xeon and AMD dual-core Opterons and uses Apache, Torque, and Maui as well as OpenMPI under CentOS 5.4.

The Scan

Shape of Them All

According to BBC News, researchers have developed a protein structure database that includes much of the human proteome.

For Flu and More

The Wall Street Journal reports that several vaccine developers are working on mRNA-based vaccines for influenza.

To Boost Women

China's Ministry of Science and Technology aims to boost the number of female researchers through a new policy, reports the South China Morning Post.

Science Papers Describe Approach to Predict Chemotherapeutic Response, Role of Transcriptional Noise

In Science this week: neural network to predict chemotherapeutic response in cancer patients, and more.