PSI Structural Genomics Knowledgebase Helen M. Berman Bottlenecks Workshop April 14, 2008.
TOPSAN – A community-driven resource for enhanced impact of structural genomics data. Protein...
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Transcript of TOPSAN – A community-driven resource for enhanced impact of structural genomics data. Protein...
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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 lifeBiological theme: Complete coverage of Thermotoga maritima
Srikrishna Subramanian
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purificationexpressioncloning
struc. refinementstruc. validationannotationpublication
phasingdata collectionxtal screening tracing xtal mounting
crystallizationimagingharvesting
targetselection
PDB
• Joint Center for Structural Genomics• One of four large scale (production) centers of PSI2• ~ 600 structures deposited in the PDB• Sustained pace of ~15 PDB depositions per month
Structure determination is done on a semi-automated assembly line
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Structure notes
We aim to describe every structure we determine.
- Introductionannotation, biology, function
- Results description of structure 2-3 figures (ribbon, active site) functional implications
- Materials and Methodsbrief protocol of all steps1 table (crystallographic stats)
- References
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…but, structure determination far outpaces our publications…
PSI-1
PSI-2
Structure collage: PSIPublication statistics : http://olenka.med.virginia.edu/psi/
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What are the reasons?• PSI rapidly solves structures of novel proteins
whose function we don't yet fully understand.• Structures are not usually associated with
extensive extant research literature. • Structures are not associated with ongoing
biochemical and biological research.• There cannot possibly be local expertise for all
proteins studied.
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Knowledge Dissemination: The Digital Age
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WEB 2.0 is reshaping how we share information:
Communities of globally distributed peers (Networks) built around rich, collaborative environments.
WikipediaCitizendiumScholarpediaGoogle Knols
TOPSANProteopediaPDBWikiOpenWetwareWikiomicsWikiProteins
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Can we have the best of all worlds?
Peer-reviewed manuscript
Automated database annotationWiki/Community
Fast, reliable,scalable
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Several existing databases/tools can assist experts to annotate protein structures.
Annotation:• Feeds from public databases• Expert-curated informationContent management:• Wiki-style editing (WYSIWYG editor)• Page-level access control• Structured fields + free text• Instant publication• Always open for comments and editsQuality control & authorship:• Encourage community collaboration• JCSG scientists & invited peers• Many authors - no contribution too
small• Lead authors (editors) in charge of
releases
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TOPSAN content:
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Protein Groups
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Browsing Options
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JCSG: Structures / Structure Notes / TOPSAN
300 of 614 JCSG structures have an annotation on TOPSAN
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Building communities
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Communities with specific biological interests
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Structural coverage of T. maritima proteome
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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: 3C8WTargetDB: 376561
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Google sent us the largest number of visitors
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UCSD & BurnhamBioinformatics CoreJohn WooleyAdam GodzikLukasz JaroszewskiSlawomir Grzechnik Sri Krishna SubramanianAndrew MorseTamara AstakhovaLian DuanPiotr KozbialDana WeekesNatasha SefcovicPrasad BurraJosie AlaoenCindy Cook
GNF & TSRICrystallomics CoreScott LesleyMark KnuthHeath KlockDennis CarltonThomas ClaytonKevin D. MurphyChristina TroutMarc DellerDaniel McMullan Polat Abdubek Claire AcostaLinda M. ColumbusJulie FeuerhelmJoanna C. HaleThamara JanaratneHope JohnsonEdward NigoghossianLinda OkachSebastian SudekAprilfawn WhiteYlva EliasGlen SpraggonBernhard GeierstangerSanjay AgarwallaCharlene ChoBi-Ying YehAnna GrzechnikJessica CansecoMimmi Brown
Scientific Advisory BoardSir Tom BlundellUniv. CambridgeHomme Hellinga
Duke University Medical CenterJames Naismith
The Scottish Structural Proteomics facility Univ. St. AndrewsJames Paulson
Consortium for Functional Glycomics,The Scripps Research Institute
Robert StroudCenter for Structure of Membrane Proteins,
Membrane Protein Expression Center, UCSF Soichi Wakatsuki
Photon Factory, KEK, JapanJames Wells
UC San FranciscoTodd Yeates
UCLA-DOE, Inst. for Genomics and Proteomics
TSRINMR CoreKurt Wüthrich Reto Horst Maggie JohnsonAmaranth ChatterjeeMichael GeraltWojtek AugustyniakPedro SerranoBill PedriniWilliam Placzek
TSRI Administrative CoreIan WilsonMarc ElsligerGye Won HanDavid MarcianoHenry TienLisa van Veen
Stanford /SSRLStructure Determination CoreKeith HodgsonAshley DeaconMitchell Miller Herbert AxelrodHsiu-Ju (Jessica) ChiuKevin JinChristopher RifeQingping XuSilvya OommachenHenry van den BedemScott TalafuseRonald ReyesAbhinav KumarChristine TrameDebanu 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
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JCSG Annual Meeting 2007