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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.

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3D-EM DAS

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  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

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