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QMPRPlus, PathArt, OEChem 1.3, Hybrid Substructure Search module (HySS), Integr8, BioPax level 1, GDAS, Ensembl

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Simulations Plus has released version 5.0 of its QMPRPlus software for predicting the pharmacological properties of potential drug molecules from their structure. New features include prediction of multiple ionization constants for molecules that have multiple ionizable atoms, and prediction of the potential for toxicity based on inhibition of estrogen binding to the estrogen receptor.


Jubilant Byiosys has released the second-quarter update of its PathArt curated pathway database. PathArt now contains 660 signaling pathways and 236 metabolic pathways and two-way integration with Spotfire’s DecisionSite and GeneSpring. A free trial of the database is available at http://www.jubilantbiosys.com.


NCBI has released a new Blast web formatter, which is available by clicking the “use new formatter” check box on the main Blast search pages (http://www.ncbi.nlm.nih.gov/BLAST/). New features include different formats for masking of low-complexity regions, as well as color-coded masking.


OpenEye Scientific Software has released OEChem 1.3, a programming library for molecular data handling. The routines can be used for a number of tasks, including file-format conversion, coordinate transformation, structural RMSD determination, substructure searching, stereochemistry recognition, and database structure clean up.


Lawrence Berkeley National Laboratory has released a new version of the Hybrid Substructure Search module (HySS) for the Phenix computational crystallography package at http://phenix-online.org/download/documentation/hyss/. The module, which automates the location of anomalous scatterers in macromolecular structures, includes an improved algorithm for the solution of small structures (less than 20 sites) given low-resolution data.


EBI has launched Integr8, a browser that integrates genomic and proteomic data for 179 species, at http://www.ebi.ac.uk/integr8. Integr8 clusters proteins for each organism according to sequence similarity, and provides views of the latest publications on an organism, as well as a list of all protein structures solved in that species, and comparisons with other species.


The BioPax (Biological Pathways Exchange) workgroup has released BioPax level 1 at http://biopax.org/Download.html. The first release of the data exchange format for pathway data is available in OWL (Web Ontology Language) and supports the representation of metabolic pathways. Subsequent levels will support molecular interaction and proteomics databases.


Affymetrix has released version 3.0 of GDAS (GeneChip DNA Analysis Software). The software includes new quality control reports; new pedigree checks; a new model-based algorithm for the GeneChip Mapping 100K Set that provides a confidence score for each genotype; batch import of pedigree information for gender identification and Mendel-error checking; the ability to export into Merlin- and GeneHunter-compatible formats; and loss-of-heterozygosity analysis.


Ensembl has released a preliminary gene build for the NCBI 35 assembly of the human genome at http://pre.ensembl.org/Homo_sapiens/. A fully annotated version of NCBI 35 is tentatively scheduled for release in September.

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The Scan

Researchers Compare WGS, Exome Sequencing-Based Mendelian Disease Diagnosis

Investigators find a diagnostic edge for whole-genome sequencing, while highlighting the cost advantages and improving diagnostic rate of exome sequencing in EJHG.

Researchers Retrace Key Mutations in Reassorted H1N1 Swine Flu Virus With Avian-Like Features

Mutations in the acidic polymerase-coding gene boost the pathogenicity and transmissibility of Eurasian avian-like H1N1 swine influenza viruses, a PNAS paper finds.

Genome Sequences Reveal Evolutionary History of South America's Canids

An analysis in PNAS of South American canid species' genomes offers a look at their evolutionary history, as well as their relationships and adaptations.

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.