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The PSI Structural Genomics Knowledge Base

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I would like to point our a unique resource for the biological NMR community, the Structural Genomics Knowledgebase (http://kb.psi-structuralgenomics.org/KB/index.jsp).

This resource is organized by Prof. Helen Berman (Director of the PDB) in collaboration with the the United States Protein Structure Initiative (PSI) and the Nature publishing group.

The KB provides comprehensive information on various aspects of structural genomics. A unique feature of the PSI-KB is the ability to blast a protein sequence against the target lists of all PSI Centers. This provides information on expression vectors, which are freely available, protocols for sample production, experimental structures, and 3D models of the target protein as well as for many homologous proteins. This is a tremendous resource for obtaining information and reagents for hypothesis-driven biology and structural biology projects.

The PSI KB also provides a portal for nominating proteins targets for structure determination by the PSI Centers: (http://kb.psi-structuralgenomics.org/KB/targetlogin.jsp) This represents a unique opportunity for biologists, or structural biologists, to obtain three-dimensional structural information on proteins they are specifically interested in.

The site also highlights recent papers from the structural biology literature, as well as papers describing recent technical advances.

Another unique feature is access to a collection of protein NMR data sets for the ongoing NMR-Critical Assessment of Protein Structure Determination Methods (NMR-CASD) project. New NMR structures are placed on hold for 8 weeks in the PDB and the corresponding chemical shift, NOESY peak list, and other data are made publicly available for testing new methods for automated NMR data analysis and/or protein structure prediction.http://kb.psi-structuralgenomics.org/KB/datasets.html

The PSI Technology Portal, linked under PSI Resources, provides descriptions of many new technologies that have been developed by the PSI project. http://kb.psi-structuralgenomics.org/KB/index1.jsp?pageshow=41

Other PSI-KB modules include Models – a data base of hundreds of thousands of homology models of protein structures, Annotation – a database of functional annotations of proteins solved in PSI project, and Metrics – a summary of metrics of success of the PSI project.

The BioMedical Themes module of the PSI-KB http://kb.psi-structuralgenomics.org/KB/index1.jsp?pageshow=85 describes the biomedical themes of the four large PSI Structure Production Centers; e.g. the primary biomedical themes of the NESG Consortium include the the network of human proteins associated with cancer biology, the several Ub and Ub-like pathways in higher eukaryotes, and the repertoires of membrane-associated lipoproteins in E coli and B subtilis, which are important antibiotic drug targets.

The PSI Knowledge Base, with links to the PSI Reagent Repository of protein expression vectors, provides a valuable resource of information and reagents that are highly enabling to protein biochemistry, cell biology, immunology, neurobiology, infectious disease, as well as proteomics and structural biology.

Gaetano Montelione

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Written by Gaetano.T. Montelione

June 23rd, 2009 at 10:43 am

Posted in Welcome