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Downloads & Upgrades: Jul 9, 2010


The Protein Data Bank in Europe (PDBe) has launched PDBeXplore, a web interface that can be used to browse, list, and analyze data in the PDB based on three classification systems: the Enzyme Classification system, the Pfam sequence-based protein-family classification system, and the CATH fold-based protein-family classification system.

Previously, PDB data was accessible "mostly by PDB accession code, or by searches based on information regarding, for instance, a publication, a molecule name, a sequence or a related 3D structure," according to the PDBeXplore developers. "While these methods are valuable for locating a specific PDB entry or group of entries, they are limited in their application and the result of such searches is usually a list of matching PDB entries and some of their attributes."

The new interface is designed to provide searching via classification systems "that are familiar and intuitive to molecular biologists, biochemists and other life scientists."

Bioclipse 2.4 is available here. The latest release of the open source workbench for workbench for chemo- and bioinformatics includes improved quantitative structure-activity relationship functionality, site-of-metabolism prediction, semantic web functionality, browsing of large compound collections, editing of chemical structures, and numerous bug fixes.

Taverna 2.2.0 is available here.

The new version includes an improved user interface and several new features, including loading and sharing of service sets, the ability to load and edit workflows that contain offline services, and the ability to report on the state of the workflow and to pause, resume, or cancel a running workflow

Taverna 2.2.0 also includes a command-line tool that allows users to execute workflows outside of the workbench.

The Scan

Two J&J Doses

Johnson & Johnson says two doses of its SARS-CoV-2 vaccine provides increased protection against symptomatic COVID-19, CNN reports.

Pfizer-BioNTech Vaccine Response in Kids

The Pfizer-BioNTech SARS-CoV-2 vaccine in a lower-dose format appears to generate an immune response among children, according to the Washington Post.

Chicken Changes to Prevent Disease

The Guardian writes that researchers are looking at gene editing chickens to help prevent future pandemics.

PNAS Papers on Siberian Dog Ancestry, Insect Reproduction, Hippocampal Neurogenesis

In PNAS this week: ancestry and admixture among Siberian dogs, hormone role in fruit fly reproduction, and more.