3d-em das extending das to 3d-em and fitting [email protected] 1 2007/02/26
TRANSCRIPT
3D-EM DAS
Extending DAS to 3D-EM and Fittinghttp://biocomp.cnb.uam.es/das/
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Molecular fitting
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High-resolution Techniques
Crystallography RMN etc.
Medium, Low-resolution Techniques
• 3D Electron MicroscopyHybrid Model
Structural DAS
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3D-EM DAS
Features /Annotations
Genomic DAS
Sequences(reference)
New
Fitting Results
(Alignment)
New
EMDBannotations
New
3D-EMvolume maps
(reference)
Structures(reference)
Alignmentserver
PeppeR3D-EM DAS
Client
New
3D-EM DAS: System [email protected]
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.
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<?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>
Reference server: [email protected]
<?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>
http://biocomp.cnb.uam.es:9000/das/3DEM/
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
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Reference server: [email protected]://biocomp.cnb.uam.es:9000/das/3DEM/
<?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>
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.
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Alignment server: [email protected]://biocomp.cnb.uam.es:9000/das/3DEM_Fitting/
Commands:
http://biocomp.cnb.uam.es:9000/das/3DEM_Fitting/entry_points
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Alignment server: [email protected]://biocomp.cnb.uam.es:9000/das/3DEM_Fitting/
<?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>
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.
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Features server: [email protected]://biocomp.cnb.uam.es:9000/das/3DEM_EMDB/
<?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>
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A new client: [email protected]
• 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.
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A new client: PeppeR
http://biocomp.cnb.uam.es/das/PeppeR/
Viewer
EMDB
PDB
UniProt
SP
ICE
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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 [email protected]
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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 [email protected]
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Acknowledgements:[email protected]
Centro Nacional de BiotecnologiaSpanish National Center for Biology
Unidad de BiocomputaciónBioComputing Unit
José Maria Carazo (head)
EMBRACE GridNetwork of excellence