TOPSAN_at_NIH

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A talk about our community based protein annotation network I gave at NIH.

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  • TOPSAN_at_NIH

    1. 1. TOPSAN – A community-driven resource for enhanced impact of structural genomics data. Protein Structure Initiative "Bottlenecks" Workshop , NIH Campus, April 14-16, 2008 Biomedical theme : Central Machinery of Life -proteins conserved in all kingdoms of life Biological theme : Complete coverage of Thermotoga maritima Srikrishna Subramanian
    2. 2. struc. refinement struc. validation annotation publication PDB <ul><li>Joint Center for Structural Genomics </li></ul><ul><li>One of four large scale (production) centers of PSI2 </li></ul><ul><li>~ 600 structures deposited in the PDB </li></ul><ul><li>Sustained pace of ~15 PDB depositions per month </li></ul>Structure determination is done on a semi-automated assembly line purification expression cloning phasing data collection xtal screening tracing xtal mounting crystallization imaging harvesting target selection
    3. 3. Structure notes <ul><li>We aim to describe every </li></ul><ul><li>structure we determine. </li></ul><ul><li>- Introduction </li></ul><ul><ul><li>annotation, biology, function </li></ul></ul><ul><ul><li>- Results </li></ul></ul><ul><ul><li> description of structure </li></ul></ul><ul><ul><li> 2-3 figures (ribbon, active site ) </li></ul></ul><ul><ul><li> functional implications </li></ul></ul><ul><ul><li>- Materials and Methods </li></ul></ul><ul><ul><li>brief protocol of all steps </li></ul></ul><ul><ul><li>1 table (crystallographic stats) </li></ul></ul><ul><li>- References </li></ul>
    4. 4. … but, structure determination far outpaces our publications…  Structure collage: PSI Publication statistics : http://olenka.med.virginia.edu/psi/ PSI-1 PSI-2
    5. 5. What are the reasons? <ul><li>PSI rapidly solves structures of novel proteins whose function we don't yet fully understand. </li></ul><ul><li>Structures are not usually associated with extensive extant research literature. </li></ul><ul><li>Structures are not associated with ongoing biochemical and biological research. </li></ul><ul><li>There cannot possibly be local expertise for all proteins studied. </li></ul>
    6. 6. Knowledge Dissemination: The Digital Age
    7. 7. WEB 2.0 is reshaping how we share information: Communities of globally distributed peers ( Networks ) built around rich, collaborative environments. Wikipedia Citizendium Scholarpedia Google Knols TOPSAN Proteopedia PDBWiki OpenWetware Wikiomics WikiProteins
    8. 8. Can we have the best of all worlds? Peer-reviewed manuscript Automated database annotation Wiki/Community Fast, reliable, scalable
    9. 10. Several existing databases/tools can assist experts to annotate protein structures. <ul><li>Annotation : </li></ul><ul><li>Feeds from public databases </li></ul><ul><li>Expert-curated information </li></ul><ul><li>Content management : </li></ul><ul><li>Wiki-style editing (WYSIWYG editor) </li></ul><ul><li>Page-level access control </li></ul><ul><li>Structured fields + free text </li></ul><ul><li>Instant publication </li></ul><ul><li>Always open for comments and edits </li></ul><ul><li>Quality control & authorship : </li></ul><ul><li>Encourage community collaboration </li></ul><ul><li>JCSG scientists & invited peers </li></ul><ul><li>Many authors - no contribution too small </li></ul><ul><li>Lead authors (editors) in charge of releases </li></ul>
    10. 11. TOPSAN content :
    11. 12. Protein Groups
    12. 13. Browsing Options
    13. 14. JCSG : Structures / Structure Notes / TOPSAN 300 of 614 JCSG structures have an annotation on TOPSAN
    14. 15. Building communities
    15. 16. Communities with specific biological interests
    16. 17. Structural coverage of T. maritima proteome
    17. 18. The biological community can utilize PSI structures only when they are aware of them Functionally well characterized enzyme and is also a new fold. PDB ID: 3C8W TargetDB: 376561
    18. 19. Google sent us the largest number of visitors
    19. 20. UCSD & Burnham Bioinformatics Core John Wooley Adam Godzik Lukasz Jaroszewski Slawomir Grzechnik Sri Krishna Subramanian Andrew Morse Tamara Astakhova Lian Duan Piotr Kozbial Dana Weekes Natasha Sefcovic Prasad Burra Josie Alaoen Cindy Cook GNF & TSRI Crystallomics Core Scott Lesley Mark Knuth Heath Klock Dennis Carlton Thomas Clayton Kevin D. Murphy Christina Trout Marc Deller Daniel McMullan Polat Abdubek Claire Acosta Linda M. Columbus Julie Feuerhelm Joanna C. Hale Thamara Janaratne Hope Johnson Edward Nigoghossian Linda Okach Sebastian Sudek Aprilfawn White Ylva Elias Glen Spraggon Bernhard Geierstanger Sanjay Agarwalla Charlene Cho Bi-Ying Yeh Anna Grzechnik Jessica Canseco Mimmi Brown Scientific Advisory Board Sir Tom Blundell Univ. Cambridge Homme Hellinga Duke University Medical Center James Naismith The Scottish Structural Proteomics facility Univ. St. Andrews James Paulson Consortium for Functional Glycomics, The Scripps Research Institute Robert Stroud Center for Structure of Membrane Proteins, Membrane Protein Expression Center, UCSF Soichi Wakatsuki Photon Factory, KEK, Japan James Wells UC San Francisco Todd Yeates UCLA-DOE, Inst. for Genomics and Proteomics TSRI NMR Core Kurt Wüthrich Reto Horst Maggie Johnson Amaranth Chatterjee Michael Geralt Wojtek Augustyniak Pedro Serrano Bill Pedrini William Placzek TSRI Administrative Core Ian Wilson Marc Elsliger Gye Won Han David Marciano Henry Tien Lisa van Veen Stanford /SSRL Structure Determination Core Keith Hodgson Ashley Deacon Mitchell Miller Herbert Axelrod Hsiu-Ju (Jessica) Chiu Kevin Jin Christopher Rife Qingping Xu Silvya Oommachen Henry van den Bedem Scott Talafuse Ronald Reyes Abhinav Kumar Christine Trame Debanu Das The JCSG is supported by the NIH Protein Structure Initiative (PSI) Grant U54 GM074898 from NIGMS (www.nigms.nih.gov). Ex officio founding members Raymond Stevens , TSRI Susan Taylor, UCSD Peter Kuhn, SSRL/TSRI Duncan McRee, TSRI/Syrrx
    20. 21. JCSG Annual Meeting 2007

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