1 / 15

3D-EM DAS

Extending DAS to 3D-EM and Fitting http://biocomp.cnb.uam.es/das/. 3D-EM DAS. jrmacias@cnb.uam.es. 1. 2007/02/26. Why 3D-EM ?. jrmacias@cnb.uam.es. Three-Dimensional Electron Microscopy Single particle EM. 2. 2007/02/26. Molecular fitting. jrmacias@cnb.uam.es.

jin
Télécharger la présentation

3D-EM DAS

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Extending DAS to 3D-EM and Fitting http://biocomp.cnb.uam.es/das/ 3D-EM DAS jrmacias@cnb.uam.es 1 2007/02/26

  2. Why 3D-EM ? jrmacias@cnb.uam.es • Three-Dimensional Electron Microscopy • Single particle EM. 2 2007/02/26

  3. Molecular fitting jrmacias@cnb.uam.es High-resolution Techniques • Crystallography • RMN • etc. Medium, Low-resolution Techniques • 3D Electron Microscopy Hybrid Model 3 2007/02/26

  4. Genomic DAS 3D-EM DAS New Structural DAS Sequences (reference) Structures (reference) 3D-EM volume maps (reference) Alignment server New Features / Annotations Fitting Results (Alignment) New New EMDB annotations PeppeR 3D-EM DAS Client 3D-EM DAS: System architecture jrmacias@cnb.uam.es 4 2007/02/26

  5. Reference server: 3DEM http://biocomp.cnb.uam.es:9000/das/3DEM/ jrmacias@cnb.uam.es • Commands: • http://biocomp.cnb.uam.es:9000/das/3DEM/entry_points • Returns known entries from EMDB database (http://www.ebi.ac.uk/msd-srv/emsearch/) • Release date are reported also, as some entries might stay unreleased. <?xml version="1.0" standalone="no"?> <!DOCTYPE DASEP SYSTEM "http://www.biodas.org/dtd/dasep.dtd"> <DASEP> <ENTRY_POINTS href="http://bioweb:9000/das/3DEM/entry_points" version="1.0.2"> <SEGMENT id="EMD1001" class="volume_map" type="ccp4" release_date="20/06/2002">EMD1001</SEGMENT> <SEGMENT id="EMD1003" class="volume_map" type="ccp4" release_date="22/08/2002">EMD1003</SEGMENT> <SEGMENT id="EMD1004" class="volume_map" type="ccp4" release_date="29/08/2003">EMD1004</SEGMENT> <SEGMENT id="EMD1005" class="volume_map" type="ccp4" release_date="30/08/2003">EMD1005</SEGMENT> <SEGMENT id="EMD1006" class="volume_map" type="ccp4" release_date="26/09/2003">EMD1006</SEGMENT> <SEGMENT id="EMD1007" class="volume_map" type="ccp4" release_date="26/09/2003">EMD1007</SEGMENT> <SEGMENT id="EMD1008" class="volume_map" type="ccp4" release_date="26/09/2003">EMD1008</SEGMENT> <SEGMENT id="EMD1009" class="volume_map" type="ccp4" release_date="26/09/2003">EMD1009</SEGMENT> <SEGMENT id="EMD1010" class="volume_map" type="ccp4" release_date="26/09/2003">EMD1010</SEGMENT> <SEGMENT id="EMD1011" class="volume_map" type="ccp4" release_date="09/10/2002">EMD1011</SEGMENT> <SEGMENT id="EMD1012" class="volume_map" type="ccp4" release_date="10/10/2002">EMD1012</SEGMENT> <SEGMENT id="EMD1013" class="volume_map" type="ccp4" release_date="10/10/2002">EMD1013</SEGMENT> … <SEGMENT id="EMD1212" class="volume_map" type="ccp4" release_date="03/04/2007">EMD1212</SEGMENT> <SEGMENT id="EMD1213" class="volume_map" type="ccp4" release_date="03/04/2006">EMD1213</SEGMENT> </ENTRY_POINTS> </DASEP> <?xml version="1.0" standalone="no"?> <!DOCTYPE DASEP SYSTEM "http://www.biodas.org/dtd/dasep.dtd"> <DASEP> <ENTRY_POINTS href="http://bioweb:9000/das/3DEM/entry_points" version="1.0.2"> <SEGMENT id="EMD1001" class="volume_map" type="ccp4" release_date="20/06/2002">EMD1001</SEGMENT> <SEGMENT id="EMD1003" class="volume_map" type="ccp4" release_date="22/08/2002">EMD1003</SEGMENT> <SEGMENT id="EMD1004" class="volume_map" type="ccp4" release_date="29/08/2003">EMD1004</SEGMENT> <SEGMENT id="EMD1005" class="volume_map" type="ccp4" release_date="30/08/2003">EMD1005</SEGMENT> <SEGMENT id="EMD1006" class="volume_map" type="ccp4" release_date="26/09/2003">EMD1006</SEGMENT> <SEGMENT id="EMD1007" class="volume_map" type="ccp4" release_date="26/09/2003">EMD1007</SEGMENT> <SEGMENT id="EMD1008" class="volume_map" type="ccp4" release_date="26/09/2003">EMD1008</SEGMENT> <SEGMENT id="EMD1009" class="volume_map" type="ccp4" release_date="26/09/2003">EMD1009</SEGMENT> <SEGMENT id="EMD1010" class="volume_map" type="ccp4" release_date="26/09/2003">EMD1010</SEGMENT> <SEGMENT id="EMD1011" class="volume_map" type="ccp4" release_date="09/10/2002">EMD1011</SEGMENT> <SEGMENT id="EMD1012" class="volume_map" type="ccp4" release_date="10/10/2002">EMD1012</SEGMENT> <SEGMENT id="EMD1013" class="volume_map" type="ccp4" release_date="10/10/2002">EMD1013</SEGMENT> … <SEGMENT id="EMD1212" class="volume_map" type="ccp4" release_date="03/04/2007">EMD1212</SEGMENT> <SEGMENT id="EMD1213" class="volume_map" type="ccp4" release_date="03/04/2006">EMD1213</SEGMENT> </ENTRY_POINTS> </DASEP> 5 2007/02/26

  6. Reference server: 3DEM http://biocomp.cnb.uam.es:9000/das/3DEM/ jrmacias@cnb.uam.es • Commands: • New command: • http://biocomp.cnb.uam.es:9000/das/3DEM/volmap?query=EMD1017 • Returns the volume map (a link, actually) for the entry. Equivalent to dna or sequence queries in other DAS systems. • New xml document definition: • Equivalent to DASSEQUENCE <?xml version="1.0" standalone="yes"?> <!DOCTYPE DASVOLMAP SYSTEM "http://biocomp.cnb.uam.es/das/dtd/dasvolmap.dtd"> <DASVOLMAP> <VOLMAP id="EMD1017" class="volume_map" type="ccp4" version="1.0"> <LINK href="ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1017/map/emd_1017.map.gz"> ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1017/map/emd_1017.map.gz </LINK> </VOLMAP> <NOTE> NOTE: The LINK element points to the location where a 3D-EM DAS client should retrive the data for the volume map (ussully through ftp) </NOTE> </DASVOLMAP> <?xml version="1.0" standalone="yes"?> <!DOCTYPE DASVOLMAP SYSTEM "http://biocomp.cnb.uam.es/das/dtd/dasvolmap.dtd"> <DASVOLMAP> <VOLMAP id="EMD1017" class="volume_map" type="ccp4" version="1.0"> <LINK href="ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1017/map/emd_1017.map.gz"> ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1017/map/emd_1017.map.gz </LINK> </VOLMAP> <NOTE> NOTE: The LINK element points to the location where a 3D-EM DAS client should retrive the data for the volume map (ussully through ftp) </NOTE> </DASVOLMAP> 6 2007/02/26

  7. Alignment server: 3DEM_Fitting http://biocomp.cnb.uam.es:9000/das/3DEM_Fitting/ jrmacias@cnb.uam.es • An alignment server… • http://biocomp.cnb.uam.es:9000/das/3DEM_Fitting/entry_points • Returns the list of known fitting experiments. • Currently this list is manually “curated” and updated from different sources, mainly EMDB. • http://biocomp.cnb.uam.es:9000/das/3DEM_Fitting/alignment?query=ID • Where ID can be a fitting, a EMDB or PDB identifier. • …plus an annotation server: • http://biocomp.cnb.uam.es:9000/das/3DEM_Fitting/types • Returns used annotation types/categories. • http://biocomp.cnb.uam.es:9000/das/3DEM_Fitting/features?segment=FFT0014 • Reports annotations about the fitting experiment conditions: • Method and software used. • Experimentalist notes. • etc. 7 2007/02/26

  8. Alignment server: 3DEM_Fitting http://biocomp.cnb.uam.es:9000/das/3DEM_Fitting/ jrmacias@cnb.uam.es • Commands: • http://biocomp.cnb.uam.es:9000/das/3DEM_Fitting/entry_points • <?xml version="1.0" standalone="no"?> • <!DOCTYPE DASEP SYSTEM "http://www.biodas.org/dtd/dasep.dtd"> • <DASEP> • <ENTRY_POINTS href="http://biocomp.cnb.uam.es:9000/das/3DEM_Fitting/entry_points" version="1.0.2"> • <SEGMENT id="FFT0001" volume="EMD1003" structure="1eg0" size="1" subparts="No" class="alignment" type="fitting"/> • <SEGMENT id="FFT0002" volume="EMD1004" structure="1mj1" size="1" subparts="No" class="alignment" type="fitting"/> • <SEGMENT id="FFT0003" volume="EMD1005" structure="1gix" size="1" subparts="No" class="alignment" type="fitting"/> • <SEGMENT id="FFT0004" volume="EMD1005" structure="1giy" size="1" subparts="No" class="alignment" type="fitting"/> • <SEGMENT id="FFT0005" volume="EMD1006" structure="1m16" size="1" subparts="No" class="alignment" type="fitting"/> • <SEGMENT id="FFT0006" volume="EMD1006" structure="1mvr" size="1" subparts="No" class="alignment" type="fitting"/> • <SEGMENT id="FFT0007" volume="EMD1007" structure="1m16" size="1" subparts="No" class="alignment" type="fitting"/> • <SEGMENT id="FFT0008" volume="EMD1007" structure="1mvr" size="1" subparts="No" class="alignment" type="fitting"/> • <SEGMENT id="FFT0009" volume="EMD1008" structure="1m16" size="1" subparts="No" class="alignment" type="fitting"/> • <SEGMENT id="FFT0010" volume="EMD1008" structure="1mvr" size="1" subparts="No" class="alignment" type="fitting"/> • <SEGMENT id="FFT0011" volume="EMD1009" structure="1m16" size="1" subparts="No" class="alignment" type="fitting"/> • <SEGMENT id="FFT0012" volume="EMD1009" structure="1mvr" size="1" subparts="No" class="alignment" type="fitting"/> … • <SEGMENT id="FFT0106" volume="EMD1213" structure="2fn2" size="1" subparts="No" class="alignment" type="fitting"/> • <SEGMENT id="FFT0107" volume="EMD1213" structure="2msb" size="1" subparts="No" class="alignment" type="fitting"/> • <SEGMENT id="FFT0108" volume="EMD1213" structure="1egi" size="1" subparts="No" class="alignment" type="fitting"/> • </ENTRY_POINTS> • </DASEP> <?xml version="1.0" standalone="no"?> <!DOCTYPE DASEP SYSTEM "http://www.biodas.org/dtd/dasep.dtd"> <DASEP> <ENTRY_POINTS href="http://biocomp.cnb.uam.es:9000/das/3DEM_Fitting/entry_points" version="1.0.2"> <SEGMENT id="FFT0001" volume="EMD1003" structure="1eg0" size="1" subparts="No" class="alignment" type="fitting"/> <SEGMENT id="FFT0002" volume="EMD1004" structure="1mj1" size="1" subparts="No" class="alignment" type="fitting"/> <SEGMENT id="FFT0003" volume="EMD1005" structure="1gix" size="1" subparts="No" class="alignment" type="fitting"/> <SEGMENT id="FFT0004" volume="EMD1005" structure="1giy" size="1" subparts="No" class="alignment" type="fitting"/> <SEGMENT id="FFT0005" volume="EMD1006" structure="1m16" size="1" subparts="No" class="alignment" type="fitting"/> <SEGMENT id="FFT0006" volume="EMD1006" structure="1mvr" size="1" subparts="No" class="alignment" type="fitting"/> <SEGMENT id="FFT0007" volume="EMD1007" structure="1m16" size="1" subparts="No" class="alignment" type="fitting"/> <SEGMENT id="FFT0008" volume="EMD1007" structure="1mvr" size="1" subparts="No" class="alignment" type="fitting"/> <SEGMENT id="FFT0009" volume="EMD1008" structure="1m16" size="1" subparts="No" class="alignment" type="fitting"/> <SEGMENT id="FFT0010" volume="EMD1008" structure="1mvr" size="1" subparts="No" class="alignment" type="fitting"/> <SEGMENT id="FFT0011" volume="EMD1009" structure="1m16" size="1" subparts="No" class="alignment" type="fitting"/> <SEGMENT id="FFT0012" volume="EMD1009" structure="1mvr" size="1" subparts="No" class="alignment" type="fitting"/> … <SEGMENT id="FFT0106" volume="EMD1213" structure="2fn2" size="1" subparts="No" class="alignment" type="fitting"/> <SEGMENT id="FFT0107" volume="EMD1213" structure="2msb" size="1" subparts="No" class="alignment" type="fitting"/> <SEGMENT id="FFT0108" volume="EMD1213" structure="1egi" size="1" subparts="No" class="alignment" type="fitting"/> </ENTRY_POINTS> </DASEP> 8 2007/02/26

  9. Features server: 3DEM_EMDB http://biocomp.cnb.uam.es:9000/das/3DEM_EMDB/ jrmacias@cnb.uam.es • Commands: • http://biocomp.cnb.uam.es:9000/das/3DEM_EMDB/features?segment=EMD1017 • Annotation reefers to the whole volume, so some fields are useless: • start / end. • orientation / phase. • subparts / superparts. <?xml version='1.0' standalone='yes'?> <!DOCTYPE DASGFF SYSTEM "http://www.biodas.org/dtd/dasgff.dtd"> <DASGFF> <GFF version="1.5" href="http://biocomp.cnb.uam.es:9000/das/3DEM_EMDB/features"> <SEGMENT id="EMD1017" version="1.0" start="1" stop=""> <FEATURE id="1017" label="1017"> <TYPE id="Description" reference="no" subparts="no" superparts="no">Description</TYPE> <START>0</START> <END>0</END> <SCORE>-</SCORE> <ORIENTATION>0</ORIENTATION> <PHASE>-</PHASE> <NOTE>Sample: "DnaB.DnaC complex from Escherichia coli "; Author: "M.Barcena,T.Ruiz,L.E.Donate,S.E.Brown,N.E.Dixon,M.Radermacher,J.M.Carazo"</NOTE> <LINK href="http://www.ebi.ac.uk/msd-srv/emsearch/atlas/1017_summary.html">Retrive EMD1017 from EMDB</LINK> <GROUP id="1" type="Summary" /> </FEATURE> </SEGMENT> </GFF> </DASGFF> <?xml version='1.0' standalone='yes'?> <!DOCTYPE DASGFF SYSTEM "http://www.biodas.org/dtd/dasgff.dtd"> <DASGFF> <GFF version="1.5" href="http://biocomp.cnb.uam.es:9000/das/3DEM_EMDB/features"> <SEGMENT id="EMD1017" version="1.0" start="1" stop=""> <FEATURE id="1017" label="1017"> <TYPE id="Description" reference="no" subparts="no" superparts="no">Description</TYPE> <START>0</START> <END>0</END> <SCORE>-</SCORE> <ORIENTATION>0</ORIENTATION> <PHASE>-</PHASE> <NOTE>Sample: "DnaB.DnaC complex from Escherichia coli "; Author: "M.Barcena,T.Ruiz,L.E.Donate,S.E.Brown,N.E.Dixon,M.Radermacher,J.M.Carazo"</NOTE> <LINK href="http://www.ebi.ac.uk/msd-srv/emsearch/atlas/1017_summary.html">Retrive EMD1017 from EMDB</LINK> <GROUP id="1" type="Summary" /> </FEATURE> </SEGMENT> </GFF> </DASGFF> 9 2007/02/26

  10. A new client: PeppeR jrmacias@cnb.uam.es • Java implementation - Architecture independent • Windows • Unix / Linux • Mac Os • Starts as a stand-alone application or • Embedded in a web browser, as an applet. - Java Web Start deployment • Launched directly from a web link. • Easy version control and upgrade. • Uses AstexViewer to display maps + pdb structures together. • Features (annotations) panels from SPICE library. 10 2007/02/26

  11. Viewer EMDB PDB SPICE UniProt A new client: PeppeR jrmacias@cnb.uam.es http://biocomp.cnb.uam.es/das/PeppeR/ 11 2007/02/26

  12. A new client: PeppeR jrmacias@cnb.uam.es Some screenshots 12 2007/02/26

  13. What about future ? jrmacias@cnb.uam.es • Visual Genomics • Integrating genomics with phenotype through image techniques: • Light, Confocal and Electron Microscopy • Tomography • Visual Proteomics • Mapping spatial information to locate macromolecular “nanomachines” inside simple model organisms. 13 2007/02/26

  14. What we’ll need ? jrmacias@cnb.uam.es • NOW: • Large data sets transfer : attachments? • Avoid indirect access, through ftp • SOON: • New types of annotations • Ontology elements • Phenotypic results • Quantitative, continuous values • Integration between different types of reference data • Allowing more cross-references between different data sources. 14 2007/02/26

  15. Acknowledgements: jrmacias@cnb.uam.es Centro Nacional de Biotecnologia Spanish National Center for Biology EMBRACE Grid Network of excellence Unidad de Biocomputación BioComputing Unit José Maria Carazo (head) 15 2007/02/26

More Related