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Downloads and Upgrades: NovaFold; Variant Annotation Integrator, VHELIBS, and Cytoscape 3.0.2

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DNAStar has launched NovaFold — a protein structure prediction tool for its Lasergene Protean 3d software — that is based on I-Tasser, a software package developed by Yang Zhang's laboratory at the University of Michigan.

According to the company, NovaFold uses threading and folding algorithms developed for I-Tasser to predict the three-dimensional structures of proteins.


The genome browser group at the University of California, Santa Cruz has launched the Variant Annotation Integrator, a new tool that helps researchers annotate and prioritize variant calls from sequencing projects,

Given a set of variants uploaded as a custom track to the browser, the VAI will return the predicted functional effect — synonymous, missense, frameshift, and intronic — for each variant. The VAI can also optionally add other types of relevant information, including: the dbSNP identifier if the variant is found in dbSNP, protein damage scores for missense variants from the Database of Non-synonymous Functional Predictions, and conservation scores computed from multi-species alignments.


Researchers at the University of Rovira i Virgili and the Technological Center of Nutrition and Health have launched the Validation Helper for Ligands and Binding Sites, or VHELIBS, a new tool for assessing the quality of ligands and binding sites in crystallographic models from the Protein Data Bank.

VHELIBS features include the ability to use different parameters to filter good models, and adjust threshold values; the flexibility to work with an unlimited number of PDB or UniProtKB codes; and the ability to choose between models from PDB_REDO or from the PDB. Researches can use the tool to choose structures where both the binding site and the ligand are well modeled, in order to validate the performance of different protein-ligand docking programs and to obtain well-modeled ligand coordinates in order to evaluate the performance of 3D conformation-generator software among other uses.


Cytoscape 3.0.2 is available here.

This release contains 14 more apps than the 3.0.0 release of the tool as well as improvements in documentation and internal organization that will be of interest to developers.

Additional details are available here and in the release notes.

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