The National Center for Biotechnology Information has released RefSeq 10 at ftp://ftp.ncbi.nih.gov/refseq/release/. The release includes genomic, transcript, and protein data available as of March 6, 2005, and includes 1,893,478 proteins and sequences from 2,827 different organisms. NCBI has also made build 1.1 of the cow genome assembly available in Map Viewer at http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=9913.
Ensembl 30 is now available at http://www.ensembl.org. The release includes a new rat assembly (assembly version 3.4 from the Rat Genome Sequencing Consortium), a new cDNA database for human based on EMBL and RefSeq data, patches to variation databases, and a merge of the est and estgene databases.
OpenEye Scientific Software has released SZYBKI 1.0. Szybki (pronounced shib'kee), means "fast" in Polish. The software uses the Merck Molecular Force Field, either with or without solvent effect, to yield 3D molecular structures. According to OpenEye, SZYBKI also refines portions of a protein structure and optimizes ligands within a protein active site, making it useful in conjunction with docking programs.
The Intelligent Systems and Bioinformatics Laboratory at Wayne State University has released Pathway-Express, a new feature in the Onto-Tools software package, at http://vortex.cs.wayne.edu/Projects.html. The software shows where genes are located on pathways, calculates impact factors for all pathways and orders them accordingly, and allows users to browse pathways and genes. A paper describing the tool is in press for the July issue of Nucleic Acids Research.
Tripos has released Lithium 2.1. The latest version of the company's 3D molecular data desktop tool includes two components: Lithium Base, an enterprise platform that allows users to automate repetitive tasks through automatically generated procedures; and Lithium Developer, a platform that supports custom interfaces and applications.