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 http://www.simbiosys.ca.
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 http://www.teranode.com.
Axiom Discovery has released Molecule Viewer, a molecular structure viewer, as a free download at http://www.axiomdiscovery.com/Downloads.htm. 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 http://sledgehmmer.sdsc.edu/.
JAligner 0.8, an open source Java implementation of the Smith-Waterman alignment algorithm, is available at http://jaligner.sourceforge.net. 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 ftp://ftp.ebi.ac.uk/pub/databases/embl/release/ (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 ftp://ftp.ncbi.nih.gov/refseq/release/. It includes 1,050,975 proteins and sequences from 2,467 different organisms. NCBI has also posted dbSNP build 121 at ftp://ftp.ncbi.nih.gov/snp/, and a new GEO Dataset cluster analysis tool at http://www.ncbi.nlm.nih.gov/geo/info/cluster.html.