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HMMer, Cytoscape 2.5.0, UniProt Release 12, Protein Data Bank, ADMET Predictor 2.3

This week at the 15th annual Intelligent Systems in Molecular Biology conference, held jointly with the 6th annual European Conference on Computational Biology in Vienna, CLC Bio showcased its accelerated version of the HMMer protein sequence-analysis algorithm, which runs on its SIMD-based CLC Bioinformatics Cell platform. According to the company, its implementation offers a 25-fold speedup for HMMer searches. The implementation works with a graphical interface through the company’s CLC Combined Workbench, or through a command-line interface. It is compatible with Mac OS X, Windows, and Linux.

Cytoscape 2.5.0, an open-source network visualization suite, contains new features such as a redesigned VizMapper interface that allows users to customize their visual styles; a redesigned filters interface for improved criteria-based selection; a Plugin Manager for installing, updating, and removing Cytoscape plugins; and a Layout Manager for controlling layout parameters.

The Uniprot Consortium has released UniProt Release 12. The new version includes 4,949,164 UniProtKB entries, including 276,256 in the UniProtKB/Swiss-Prot section and 4,672,908 in the UniProtKB/TrEMBL section.

The Research Collaboratory for Structural Bioinformatics said this week that on Aug. 1 it will release a “remediated” version of the Protein Data Bank archive, which removes a number of inconsistencies that have been introduced over the years. The archive, which will be available here, will include standardized IUPAC nomenclature for chemical components as well as updated sequence references to databases and taxonomies, resolved differences between chemical and macromolecular sequences, updated primary citation assignments, and other features. 
RSCB said that users may have to download new software to view the files with the new nomenclature. Further information on the new software requirements is available here.

Simulations Plus has released ADMET Predictor 2.3, which includes more accurate predictive models that have been retrained “with an enhanced set of molecular descriptors,” the company said. The software also includes a new feature for predicting whether a drug-like molecule is likely to cause mutations in Salmonella strains that the FDA requires for mutagenicity testing.

Filed under

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