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SRS everEST 1.0, ProteomWeaver, EMBL-Align, WEBIN-Align, PDB Validation Suite


Lion Bioscience of Heidelberg, Germany, has launched SRS everEST 1.0 for transcript reconstruction. The software clusters ESTs using Electric Genetics’ stackPACK clustering system. SRS everEST is linked to Lion’s SRS data integration system to enable the assignment of biological information to gene sequences.

Lion said it has already sold SRS everEST to customers including Nestle and Intervet Innovation.


Definiens, an image analysis software company based in Munich, has released ProteomWeaver for high-throughput 2D gel analysis, its first bioinformatics product.

The software is based on technology developed by Nobel Laureate Gerd Binnig. According to Definiens, the system can analyze an unlimited number of gels, automatically eliminate streaking, and detect spots with high precision independent of size or quantity. An alpha release of the software will be available for the company’s partners in September.


A new public alignment database, EMBL-Align, and a web-based alignment submission tool, WEBIN-Align, are now available from the European Bioinformatics Institute at and embl/Submission, respectively.

The new tool and database have an interactive web-based interface for nucleotide and protein alignment data and links to primary data in EMBL/DDBJ/Genbank and Swiss-Prot. They accept common alignment formats including Clustal, NEXUS, Phylip, FASTA, and MSF.


The Research Collaboratory for Structural Bioinformatics has made a beta version of the PDB Validation Suite available for download from The set of programs creates validation reports about 3D structure data and is designed to work with files in mmCIF or PDB format.


The University of California, Los Angeles-Department of Energy Laboratory of Structural Biology and Molecular Medicine has released JDIP, a stand-alone, Java-based browser-independent interface to the DIP (database of interacting proteins) database.

The program enables customized graph rendering, annotation, local storage, and printing of the protein interaction networks. JDIP is available at


NAMD 2.3b2, parallel object-oriented molecular dynamics code for the simulation of large biomolecular systems, is now publicly available from the Theoretical Biophysics Group at the University of Illinois at

Improvements over NAMD 2.2 include new ports to the Compaq AlphaServer SC and Scyld Beowulf and improved serial performance.


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