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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

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.