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nmr 2.0 Updates

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Dear NMR friends,

In support of the central mission of the NMR 2.0 site, which is to enable the efficient sharing and dissemination of NMR knowledge using ‘Web 2.0’ capabilities, our site was enhanced significantly since the end of 2009.

1) A search algorithm was implemented to ‘filter’ records by keywords in individual sections.

2) Tagging of records is now optional for their improved organization.

3) Subscribed users are now able to comment on individual records to share their experiences.

4) The “Google custom search engine” was incorporated and searches both NMR 2.0 and a complementary NMR wiki (http://nmrwiki.org).

5) Each record is now displayed along with an icon indicating the file type of the record (e.g., wmv, gif, jpeg, pdf, or Microsoft Word, Excel, or Powerpoint).

6) A ‘share bookmarking button’ was introduced for all records located in Resources, Links, Blog and the NESG NMR Wiki. This allows users to email records, or to share them on networking portals such as Facebook.

7) The Jobs section in Resources now also allows researchers looking for a job (‘job seekers’) to post their professional profile along with a description what kind of job they are looking for.

8) The NMR Wiki of the Northeast Structural Genomics Consortium (http://www.nesg.org) was integrated into the NMR 2.0 portal. This enables subscribed users to access both sites with a single login.

The NMR Wiki is based on the open-source Mediawiki package (http://www.mediawiki.org/wiki/MediaWiki) and comprises contributions written by NMR scientists of the Northeast Structural Genomics Consortium (NESG; http:www.nesg.org) working at Miami University (OH, USA), Rutgers University (NJ, USA), the State University of New York at Buffalo (NY, USA), University of Georgia (GA, USA), and the University of Toronto (ON, Canada). It was launched in January 2010 at the Keystone meeting on Structural Genomics.

The NESG NMR wiki serves to efficiently disseminate established protocols of the NESG high-throughput NMR structure determination pipeline, including those for protein sample preparation, NMR data acquisition, NMR data processing, NMR resonance assignment, and structure calculation, validation and deposition in the Protein Data Bank (PDB; http://www.pdb.org.

In an article (http://sbkb.org/update/2010/03/full/th_psisgkb.2010.09.html) recently posted on the Structural Biology Knowledgebase, the NESG NMR Wiki was highlighted by Maria Hodges, and the complementary nature with the ‘NMR Wiki’ project was discussed by her in a second blog article (http://woodforthetrees.wordpress.com/2010/02/22/a-tale-of-two-wikis/).

We look forward to your contributions to NMR 2.0 (which requires registration), and we welcome articles from experienced researchers for the ‘Blog’ on any issue they consider to be of importance for the NMR community. To contribute articles to the Blog, please send a brief notification to szypersk@buffalo.edu and nmradmin@buffalo.edu.

Last but not least, we truly appreciate your proposals for future improvements which can be posted at http://www.nmr2.buffalo.edu/feedback.

With best regards,

Thomas Szyperski, Professor of Chemistry

Sriram Sankaran, IT Specialist

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Written by Thomas Szyperski

February 17th, 2011 at 6:47 pm

Posted in NMR, Welcome

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

Welcome to NMR 2.0

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Dear Colleagues,

Welcome to the new NMR 2.0 web site which is supposed to help all scientists pursuing NMR-based research to share and compile information, and to foster exchange of knowledge.

It is possible to upload URLs as links, as well as files of various formats in three sections, i.e., ‘Resources’,'Links’ and ‘Entertainment’. The ‘Links’ section is eventually supposed to provide all web links which we routinely use. Since all registered users can provide links, this page may eventually provide all links that are now compile on ‘traditional’ link pages. Please note that links uploaded in the sections ‘Resources’ and ‘Entertainment’ are simultaneously introduced in the ‘Links’ section.

In addition NMR 2.0 offers ‘web 2.0′ features such as RSS feeds.

We hope that you appreciate this site and look forward to your contributions.

The blog of NMR 2.0 will be used by senior researchers to contribute articles outlining new developments, suggestions and information on issues that are of importance to the NMR Community.

Best regards,

Thomas Szyperski

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Written by Thomas Szyperski

March 27th, 2009 at 10:21 am

Posted in Welcome