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Proteomweaver 2.1., eHiTS, Pfam, MSDbar, SEQtools, PubMatrix, UCSF Chimera, MPsrch 4.2.80, human disease ontology

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Definiens has released Proteomweaver 2.1. Definiens said the updated version of its 2D gel electrophoresis analysis software uses a new quantification algorithm that is designed for multi-fluorescence gels and can detect protein expression ratios as low as 1.17 with a significance of 0.001 using two replicate gels.

 

SimBioSys has launched a new ligand docking and virtual screening program called eHiTS (electronic High Throughput Screening). Typical docking speed per ligand per CPU is a few seconds, according to the company, and the software supports parallel execution via SMP, Linux clusters, or distributed grid computing. eHiTS is currently available on Unix platforms. Further information is available at http://www.simbiosys.ca/.

 

Version 9.0 of the Pfam protein family database is available at http://www.sanger.ac.uk/Software/Pfam, http://pfam.wustl.edu, and http://www.cgr.ki.se/Pfam. Pfam 9.0 contains 5,724 protein families.

 

The Macromolecular Structure Database group at the European Bioinformatics Institute has released a toolbar application called MSDbar to search the MSD Relational Database by author name, bound ligand name/ID, PDB ID code, keyword, header, and Medline or SwissProt accession numbers. It is available at http://www.ebi.ac.uk/msd-srv/docs/msdbar.html.

 

Søren Rasmussen, a bioinformatics researcher at H. Lundbeck in Denmark, has released SEQtools version 8.0.760, a free software package for sequence analysis, at www.seqtools.dk.

 

The National Institute on Aging has released PubMatrix, a free web-based PubMed literature-mining tool, at http://pubmatrix.grc.nia.nih.gov/.

 

The UCSF Resource for Biocomputing, Visualization, and Informatics has released a new version of UCSF Chimera, an interactive molecular modeling system, at http://www.cgl. ucsf.edu/chimera. It is free to academic and non-profit users and is available for Windows, Linux, Mac OS X, Irix, and Tru64 Unix.

 

MPsrch 4.2.80, a fast implementation of the Smith-Waterman algorithm, is available from EBI at http://www.ebi.ac.uk/MPsrch/index.html. The implementation was done in collaboration with Aneda.

 

Northwestern University has released a draft human disease ontology at http://diseaseontology.sourceforge.net. The defined vocabulary organizes human diseases into a framework to facilitate mining of human health records and to aid the association with genome information.

 

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