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PSI Debuts Web Portal to Aggregate Data


The Protein Structure Initiative, a public-private venture that began in 2000 to determine the three-dimensional atomic structures of all proteins, has launched a new Web-based resource to complement existing databases by providing a single access point to all information associated with high-throughput structure-determination experiments.

The PSI Structural Genomics Knowledgebase, which aims to help scientists cross-mine a variety of information compiled by a dozen PSI research groups, went live last month. With a total budget of $2.5 million, it will enable all researchers to study proteins of interest or a particular aspect of structural genomics.

To date, PSI scientists have solved 2,800 protein structures and deposited them in the Protein Data Bank, which now holds 49,000 experimentally determined structures. The PSI Knowledgebase, for its part, will expand beyond the PDB by focusing on the experimental processes that led PSI researchers to obtain their structures, says Helen Berman, a bioinformaticist and chem-ist at Rutgers University and director of the PDB.

"The PSI scientists produce, of course, structures, but they also produce methodologies for doing the structures that are very, very rapid," says Berman, who helped devise the PSI Structural Genomics Knowledgebase and is its director. The idea now is to organize the way information can be shared and mined prior to structure resolution and thus help avoid bottlenecks and scientific cul-de-sacs.

The PSI had always comprised a large number of centers "hacking along" and producing structures, says Bernhard Rupp, founder and CEO at crystallography firm QED Life Science Discoveries and one-time head of drug target crystallography at Lawrence Livermore National Laboratory. However, every center placed its data in a different location, sometimes in a different format, with different identifiers, which was "a complete mess if you wanted to do large-scale data-mining," he says.

— Vivien Marx 

Bioinformatics Notes

Current BioData will open a new research and publishing center in Wales to serve customers in the US, Europe, and other regions. The company currently markets a curated protein database, which is updated on a daily basis.

BioDiscovery has announced that the National Cancer Institute has obtained a site license for its Nexus Copy Number software. The software can integrate microarray data with their clinical annotations in a single project.

Johnson & Johnson Pharmaceutical Research and Development has extended a licensing agreement for BioWisdom's OmniViz visualization and data-mining software. It can visualize text, numerical, and categorical data as well as genome sequences, chemical structures, and text files.


Germany's Technische Universitat Dresden Got an SGI Altix cluster that will be Used in bioinformatics Research. The 11.9-teraflop SGI Altix 4700 system Runs on a 2,048 Intel Itanium 2 processor core. 

Funded grants

Database of Functional SNPs in Cancer-Related, Environmentally Responsive Genes
Grantee: Yong Zhu, Yale University
Begins: Mar. 1, 2007; Ends: Feb. 28, 2010 
With this grant, Zhu and his team will continue to explore the application of available bioinformatics methods in functional SNP selection. This project aims to identify SNPs with potential functional importance in roughly 700 environmentally responsive genes. The researchers plan to construct a functional SNP database to survey SNP functionality and roles in cancer case-control studies. 

Computational Drug Discovery with Polarizable Potential Energy Function
Grantee: Pengyu Ren, University of Texas-Austin
Begins: Sep. 1, 2007; Ends: July 31, 2012
Ren will use this funding to develop computational techniques for drug discovery based on accurate prediction of ligand-protein interactions using a novel, polarizable potential energy function. Ren and his colleagues hope that the resulting programs will be compatible with existing drug discovery and molecular modeling software.

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