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

2. 2 Three-Dimensional Electron Microscopy Single particle EM. Why 3D-EM ? jrmacias@cnb.uam.es

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

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

5. 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. 5 2007/02/26 EMD1001 EMD1003 EMD1004 EMD1005 EMD1006 EMD1007 EMD1008 EMD1009 EMD1010 EMD1011 EMD1012 EMD1013 … EMD1212 EMD1213 Reference server: 3DEM jrmacias@cnb.uam.es EMD1001 EMD1003 EMD1004 EMD1005 EMD1006 EMD1007 EMD1008 EMD1009 EMD1010 EMD1011 EMD1012 EMD1013 … EMD1212 EMD1213 http://biocomp.cnb.uam.es:9000/das/3DEM/

6. 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 6 2007/02/26 Reference server: 3DEM jrmacias@cnb.uam.es http://biocomp.cnb.uam.es:9000/das/3DEM/ ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1017/map/emd_1017.map.gz 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) ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1017/map/emd_1017.map.gz 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)

7. 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 Alignment server: 3DEM_Fitting jrmacias@cnb.uam.es http://biocomp.cnb.uam.es:9000/das/3DEM_Fitting/

8. Commands:  http://biocomp.cnb.uam.es:9000/das/3DEM_Fitting/entry_points 8 2007/02/26 Alignment server: 3DEM_Fitting jrmacias@cnb.uam.es http://biocomp.cnb.uam.es:9000/das/3DEM_Fitting/ … …

9. 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. 9 2007/02/26 Features server: 3DEM_EMDB jrmacias@cnb.uam.es http://biocomp.cnb.uam.es:9000/das/3DEM_EMDB/ Description 0 - 0 - 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" Retrive EMD1017 from EMDB Description 0 - 0 - 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" Retrive EMD1017 from EMDB

10. 10 2007/02/26 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.

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

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

13. 13 2007/02/26 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. What about future ? jrmacias@cnb.uam.es

14. 14 2007/02/26 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. What we’ll need ? jrmacias@cnb.uam.es

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