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How to Use the PSI Structural Genomics Knowledgebase for Research Part II: Demonstration

How to Use the PSI Structural Genomics Knowledgebase for Research Part II: Demonstration. 2009 NIGMS Workshop: Enabling Technologies for Structural Biology Section on Structural Analysis Margaret J. Gabanyi March 4, 2009.

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How to Use the PSI Structural Genomics Knowledgebase for Research Part II: Demonstration

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  1. How to Use the PSI Structural Genomics Knowledgebase for ResearchPart II: Demonstration 2009 NIGMS Workshop: Enabling Technologies for Structural Biology Section on Structural Analysis Margaret J. Gabanyi March 4, 2009

  2. The PSI SGKB homepage makes many features available from one central place.

  3. The Structural Genomics Update provides a collection of PSI and broader research highlights, news, and events in collaboration with the Nature Publishing Group

  4. About this site About this site contains instructions, FAQs, and also academic exercises on how to use the SGKB. URL: http://kb.psi-structuralgenomics.org/KB/KB-Tour.html

  5. About PSI PSI Policies, Reports, administrative, and funding opportunities are located on the About PSI site.

  6. PSI Centers The PSI centers menu shows information about the PSI-2 Network centers, their objectives, and a link to their homepages.

  7. PSI Resources In addition to the search function, you can visit each of the PSI resources individually. Links point to more information about the resource and its homepage.

  8. PSI Resource: Technology Portal

  9. NPG Resources Links to Nature resources, such as the Nature Gateways, NPG Journals, and bookmarking and blog tools are also made available here.

  10. Subscribe to RSS feeds Users can subscribe to E-alerts and RSS (Really Simply Syndication) feeds to automatically receive notice of PSI SGKB content and latest structure updates

  11. Functional Sleuth In Functional Sleuth, we present protein structures determined by the PSI structural genomics efforts whose further functional analysis is required.

  12. Functional Sleuth

  13. Community-Nominated Targets The greater scientific community is invited to submit protein target nominations for structure determination using the Community-Nominated Targets proposal system.

  14. Latest PSI Structures and Statistics You can see latest structures solved by the PSI Centers; this list can also be delivered to your browser weekly using a (Really Simple Syndication) RSS feed.

  15. Latest PSI Statistics

  16. Structural Genomics Update • Research Advances Editorials about recent structure and technological results • Featured Molecule Detailed explanation about a PSI structure • Research Library Catalog of PSI and other papers about the protein production and structural determination pipeline • News • Events Calendar

  17. Research Advances Editorials about recent Research Advances such as new structures and technical highlights are provided by the Nature Publishing Group

  18. Research Advances Research Advances editorials contain links that directly query the PSI SGKB, and the main search box is available to query other topics.

  19. Featured PSI Molecule Each month, the Featured PSI Moleculegives a detailed portrait of a biological molecule solved by the PSI structural genomics efforts.

  20. Featured PSI Molecule The Featured PSI Molecule is an article about a PSI structure written by David Goodsell in his easily accessible style.

  21. Research Library The Research Library is a catalog of all PSI and other publications to date related to the protein production and structure determination pipeline. Structural and functional reports are found here as well.

  22. Research Library

  23. News and Events Calendar To present a broader update on recent scientific advances, we provide the latest News from the Protein Structure Initiative, Nature News and other NPG publications. An Events Calendar keeps the community in touch with upcoming conferences, events, and workshops that promote a structural view of biology.

  24. Sequence/PDB ID search and results • Availablestructures of proteins with similar/identical amino acid sequences • Any structural and functional properties (annotation) determined from these protein structures • Homology models created for/with your query sequence • Information about similar protein sequences (targets) studied by the PSI structural genomics efforts • The protocols used during those PSI research efforts • Ordering information to obtain DNA clone materials, if available

  25. Structures Tab

  26. Annotations Tab

  27. Models Tab

  28. Targets Tab

  29. Protocols Tab

  30. Materials Tab

  31. Text Search With a plain text search, gain access to information from: • PSI Center web pages • Publications resource • Technology resource • Annotation database

  32. Text search results

  33. For Further Information PSI SGKB http://kb.psi-structuralgenomics.org PSI SGKB Tutorial http://kb.psi-structuralgenomics.org/KB/KB-Tour.html PSI SGKB Tutorial with classroom exercises http://kb.psi-structuralgenomics.org/KB/KB-Tutorial.html

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