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Downloads & Upgrades: Jun 11, 2010


Oregon State University has released a new version of the Protein Geometry Database, a resource that allows users to explore either protein conformation or protein covalent geometry or the correlations between protein conformation and bond angles and lengths.

The new version includes the ability to compose queries and analyze the behavior of side chain chi angles.

In addition, the PGC includes structures released in the wwPDB as of April 8, including approximately 18,000 nonredundant protein chains from crystal structures.

Simcyp has released version 10.0 of the Simcyp Population-based ADME Simulator.

The new version includes the ability to include transporter interactions and clinical inputs in predicting drug-drug interactions. The software also includes improvements in the Advanced Dissolution, Absorption, and Metabolism model "to allow users to investigate the influence of different drug release formulations or dissolution profiles on the level of DDIs along the gut," the company said.

Kinexus Bioinformatics has expanded its PhosphoNet KnowledgeBase. The free resource now includes data on more than 92,000 human phosphorylation sites, including their occurrence in over 20 other diverse species, and identification of the protein kinases that target these regulatory sites.

Italy's Magna Graecia University has released Cytomcl, a Cytoscape plug-in for clustering networks using the Markov cluster algorithm, an unsupervised clustering algorithm for graphs.

The Scan

Just Breathing

A new analysis suggests that most Mycobacterium tuberculosis is spread by aerosols from breathing, rather than by coughing, the New York Times reports.

Just Like This One

NPR reports that the World Health Organization has hired a South African biotech company to recreate mRNA vaccine for SARS-CoV-2 that is similar to the one developed by Moderna.

Slow Start

The Wall Street Journal reports that Biogen's Alzheimer's disease treatment had revenues for July through September that totaled $300,000.

Genome Research Papers on Cancer Chromatin, Splicing in the Thymus, Circular RNAs in Cancer

In Genome Research this week: analysis of bivalent chromatin sites, RBFOX splicing factors' role in thymic epithelial cells, and more.