Tripos has released Advanced Protein Modeling, a software package that combines methods for homolog identification, sequence alignment, and interactive comparative protein structure modeling. Advanced Protein Modeling is available as an optional component of Sybyl 7.3, and is based on the Fugue and Orchestrar technologies developed by Tom Blundell’s lab at the University of Cambridge. Further information on Advanced Protein Modeling is available here.
The US Department of Energy’s Joint Genome Institute has released Integrated Microbial Genomes 2.0. The release includes 1,541 new microbial, viral, and eukaryotic genomes, bringing the total to 2,301 (595 bacterial, 32 archaeal, and 13 eukaryotic genomes, as well as 1,661 viruses). Of these, 2,058 are finished and 243 are draft. IMG 2.0 also includes gene-based links to NCBI's Entrez Gene, Lawrence Berkeley National Laboratory's MicrobesOnline, and Argonne National Laboratory's PUMA.
The National Center for Biotechnology Information has released its annotation of the chicken genome assembly, build 2.1. The data can be viewed in Map Viewer here or downloaded by ftp here.
The European Bioinformatics Institute has released an updated version of the International Protein Index database here. The database, compiled from UniProt, RefSeq, Ensembl, TAIR, and H-InvDB, includes protein data for human, mouse, rat, zebrafish, Arabidopsis, chicken, and cow.
The Fox Chase Cancer Center has released ProtBuD, a database of information on asymmetric units and hypothetical biological units as obtained from the Protein Data Bank and the EBI’s Protein Quaternary Server. Users can query by PDB entry codes to retrieve ASU and BU information across the family or superfamily as defined by SCOP and PSI-BLAST relationships. The database can also be used to search for specific content across a family or superfamily, such as complexes with ions, ligands, or nucleic acids. According to the developers, biological units from the PDB or PQS differ from the asymmetric unit for 52 percent of X-ray structures, while PQS and PDB biological units disagree with each other for 18 percent of X-ray entries.
BiOpiniO Systems Biology has released iTMs, a manually curated collection of functional and disease-centered networks. The iTMs collection includes information on more than 25 biological mechanisms and more than 10 neurodegenerative and autoimmune diseases. The company said it plans to expand iTMs to more than 100 networks in the near future.
SCOP (Structural Classification of Proteins) 1.71 is available here. The release includes 27,599 PDB entries and 75,930 domains.
IO Informatics has released Sentient Suite 2.95. The latest version of the data-integration system includes performance enhancements, more options for importing spreadsheet data, XML data integration, an intuitive query interface, and the capability to tag sample data with barcodes or RFIDs
Bioperl 1.5.2, a developer release, is available here. New features include an “overhaul” of the taxonomy (Bio::Species), module, and improvements in Bio::Map and Bio::SearchIO.
Version 2.6.0 of the Open Microscopy Environment is available here. The release includes an improved web interface, access control, and connectivity with other applications. It also offers two-way integration with Excel to enable the population of spreadsheets directly from a live OME server using a VisualBasic library included in src/Excel/OME-Excel.xls. OME 2.6.0 also offers improved connectivity with Matlab.
CABIN (Collective Analysis of Biological Networks), a Cytoscape plug-in that allows exploratory data analysis of multiple interaction networks, is available from the Pacific Northwest National Laboratory here. CABIN enables integration and analysis of interactions from multiple sources.