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Ciphergen Biosystems, SwissProt, Protein Data Bank


Ciphergen Biosystems has released, in conjunction with Salford Systems, Biomarker Patterns Software 5.0 for the elucidation of clinically relevant protein patterns. The software is based upon a recently issued patent for finding protein patterns in mass spectra using a classification and regression tree algorithm (see PM 2-20-04). The software is intended for use with Ciphergen’s SELDI ProteinChip system. Ciphergen and Salford collaborated to create the software by modifying Salford’s existing Classification and Regression Tree procedure. Ciphergen holds exclusive rights to the technology. A new component to Biomarker Patterns Software 5.0 is an intelligent feature selection using functionality from Salford’s TreeNet algorithm. TreeNet builds a large number of small trees that each corrects the errors of its predecessors. This helps avoid the potential problem of over-trained data sets, according to Ciphergen.

The software “sets Ciphergen’s proteomics platform apart from groups that are using other pattern recognition methods without protein ID and from groups cataloguing protein IDs for literature validation in order to guess which protein will make a good assay — a classical approach which has had limited success in developing in vitro diagnostic tests over the past decades,” Martin Verhoef, president of Ciphergen’s Biosystems Division, said in a statement.

Version 43.0 of SwissProt is now available for access at the website The release contains 146,720 fully annotated sequences and 54,093,154 amino acids.

The Protein Data Bank is making available a new QuickSearch keyword search feature. The new feature supports searches across the PDB archive and website static pages.


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