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eHiTS 4.3, VLX Design Suite 1.4, Molecule Viewer, Sledge-Hmmer, JAligner 0.8, EMBL Nucleotide Sequence Database, PEAKS 2.4, SilicoCyte, RefSeq 6, dbSNP build 121, GEO Dataset cluster analysis tool


SimBioSys has released eHiTS 4.3, a ligand-docking package for the Linux and SGI platforms. The new version of the software includes improved multi-threading computations to decrease the overall wait times for dockings, the company said. A demo version is available at


has released VLX Design Suite 1.4, which includes new support for SBML (Systems Biology Markup Language) Level 2. The software allows researchers to create biochemical models and then export and share them using SBML. VLX Design Suite 1.4 is available for trial at

Axiom Discovery has released Molecule Viewer, a molecular structure viewer, as a free download at The software allows users to view molecular structures in various file formats, including PDB, Alchemy, MDL, Gaussian, MOPAC, and others.

The San Diego Supercomputer Center has launched the Sledge-Hmmer web server, which enables genome-scale searching of the Pfam protein family database. The server and downloadable data can be found at

JAligner 0.8, an open source Java implementation of the Smith-Waterman alignment algorithm, is available at New features include the ability to run as a desktop application, new editing capabilities, and support for input sequences in plain text in addition to the Fasta format.

Release 80 of the EMBL Nucleotide Sequence Database is available from (UK) and mirror sites. Release 80 is about 35.5 gigabytes compressed and 201 gigabytes uncompressed.

Bioinformatics Solutions has released version 2.4 of its PEAKS protein and peptide analysis software. The new version has been optimized for Fourier transform ion cyclotron resonance mass specs.

CytoGenomics said that its SilicoCyte microarray platform now supports the import of single-channel image analyzed data exported from Affymetrix’s MAS Suite 5.0 as well as from Axon’s GenePix Pro.

The National Center for Biotechnology Information has released RefSeq 6 at It includes 1,050,975 proteins and sequences from 2,467 different organisms. NCBI has also posted dbSNP build 121 at, and a new GEO Dataset cluster analysis tool at

Filed under

The Scan

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.

Machine Learning Improves Diagnostic Accuracy of Breast Cancer MRI, Study Shows

Combining machine learning with radiologists' interpretations further increased the diagnostic accuracy of MRIs for breast cancer, a Science Translational Medicine paper finds.

Genome Damage in Neurons Triggers Alzheimer's-Linked Inflammation

Neurons harboring increased DNA double-strand breaks activate microglia to lead to neuroinflammation like that seen in Alzheimer's disease, a new Science Advances study finds.

Long COVID-19 Susceptibility Clues Contained in Blood Plasma Proteome

A longitudinal study in eBioMedicine found weeks-long blood plasma proteome shifts after SARS-CoV-2 infection, along with proteomic signatures that appeared to coincide with long Covid risk.