embo workshop, 26 sept. 2008 tutorials for pdbj search tools · xpsss (xml-based protein structure...
TRANSCRIPT
![Page 1: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/1.jpg)
http://www.pdbj.org/http://www.protein.osaka-u.ac.jp/rcsfp/pi/
Haruki NakamuraInstitute for Protein Research,
Osaka University
Tutorials for PDBjSearch Tools
EMBO workshop, 26 Sept. 2008
![Page 2: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/2.jpg)
Protein Data Bank Japan
http://www.pdbj.org/
At Institute for Protein Research, Osaka Univ. since 2001 supported from the Institute for Bioinformatics Research and Development, Japan Science and Technology Agency (BIRD-JST).
Structure Data curationand editing
Structure Data browsing and downloading
![Page 3: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/3.jpg)
PDBj members at IPR, Osaka Univ.
![Page 4: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/4.jpg)
http://www.pdbj.org/
![Page 5: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/5.jpg)
Processed data numbers at PDBj
0
2000
4000
6000
8000
1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 31 33 35
Yearly wwPDB processed numberYearly PDBj processed number
Yea
rly
regi
stra
tion
num
ber 8000
6000
4000
2000
01972 75 80 85 90 95 2000 2007
We process 25-30 % deposited data of the entire world, mainly from Asian and Oceania regions
Total 52,535 on August 19, 2008
year
![Page 6: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/6.jpg)
http://www.pdbj.org/
![Page 7: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/7.jpg)
Get Entry DataAccess to http://www.pdbj.org/
Summary for each PDBID is displayed.
PDBID (e.g. 1gof) should be input in a box and GO
![Page 8: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/8.jpg)
Get Entry DataAccess to http://www.pdbj.org/
Summary for each PDBID
![Page 9: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/9.jpg)
Graphic viewer: jV version 3.6Access to http://www.pdbj.org/jV/
![Page 10: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/10.jpg)
![Page 11: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/11.jpg)
Several Information for each Entry: Structural Details
Name of the molecule(s)
Molecular weight(s)
Keywords
etc.
Details of the structure
![Page 12: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/12.jpg)
Several Information for each Entry: Experimental Details
Experimental method
(X-ray, NMR, EM, Neutron)
Parameters for the crystal
Crystallization conditions
etc.
Details of the experiment
![Page 13: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/13.jpg)
Several Information for each Entry: Functional Details
Gene ontology information
Ligand binding
Functional site
etc.
Details of the function
![Page 14: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/14.jpg)
Several Information for each Entry: Sequence Neighbor
Result of BLAST search
Sequence Navigator is used.
PDBID list of homologs
![Page 15: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/15.jpg)
Several Information for each Entry: Download/Display
Conventional PDB format
Conventional PDB header
mmCIF
PDBML
PDBML without coordinates
PDBML for only coordinates
Structure factor
Download or display of the archival data
![Page 16: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/16.jpg)
Several Information for each Entry: Link
RCSB-PDB, MSD-EBI
CATH, SCOP, FSSP: folds
UniProt: Sequences
KEGG: Pathways
EzCatDB: enzymes
etc.
Link to other databases
![Page 17: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/17.jpg)
Advanced SearchFrom "Advanced Search" on Top page
Author names & Journal
Experimental method
Ligand name
Residues
Resolution
Species
etc.
Search by many conditions
![Page 18: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/18.jpg)
XQuery/XPath SearchFrom “xPSSS (xml-based Protein Structure Search Service)” page
XML based search
XQuad: help by XQuery advisor
Search by XQuery/XPath
![Page 19: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/19.jpg)
Search for all entries with helix of length equal to 10 residues:
![Page 20: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/20.jpg)
XQuad: XQuery Advisor
![Page 21: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/21.jpg)
XQuad: XQuery Advisor
![Page 22: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/22.jpg)
List of hit PDBIDs is displayed.
Search of Similar Sequences:Sequence Navigator
PDBID or amino-acid sequence should be input and "Find All Homologs"
![Page 23: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/23.jpg)
Structural alignment: GASH
PDBID or PDB-format file name should be input and "Superimpose"
The optimal structural alignment is displayed.
![Page 24: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/24.jpg)
Search of Similar Structures:Structure Navigator
PDBID should be input and "Start Structure Navigator"
List of hit PDBIDs is displayed.
![Page 25: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/25.jpg)
Total number in PDBMLplus 52,535
GO Information (Biological Process, Molecular Function, Cellular Component) 20,186
Extracted from Literatures by Annotators 20,040
Information of binding site residues from HETATM 29,006
Function Information from Uni-Prot(ACT_SITE, BINDING, DNA_BIND, NP_BIND, ZN_FING, TRANSMEM)
28,243
Function Information from CATRES/extCATRES-EBI-CSA-EBI-
3,17418,668
Primary Citation Information 48,968
Additional Information in our XML databse: PDBMLplus
(as of August 19, 2008)
![Page 26: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/26.jpg)
Addition of Data in PDBMLplus<exptl>
<method>SYNCHROTRON RADIATION</method><crystal id="1"><grow auth_validate="N" update_id="6">
<method auth_validate="N" update_id="6">Microdialysis</method><temp auth_validate="N" unit="&#x2103;" update_id="6">4</temp><pH auth_validate="N" update_id="6">4</pH>
</grow>
<grow_comp id="1" auth_validate="N" update_id="6"><sol_id auth_validate="N" update_id="6">1</sol_id><name auth_validate="N" type="common name" update_id="6">protein</name><conc auth_validate="N" unit="mg/ml" update_id="6">13</conc>
</grow_comp>
<grow_comp id="2" auth_validate="N" update_id="6"><sol_id auth_validate="N" update_id="6">2</sol_id><name auth_validate="N" type="common name" update_id="6">ammonium
sulphate</name><conc auth_validate="N" unit="%sat" update_id="6">70</conc>
</grow_comp>::
</crystal></exptl>
![Page 27: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/27.jpg)
Example for 12as with the functional site information
![Page 28: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/28.jpg)
Command:
show xps3
Advanced usage of jV version3 with xPSSS
![Page 29: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/29.jpg)
xPSSS (xml-based Protein Structure Search Service)
PDBML
PDBMLplus
Web server
XSLT processor
downloader
Loader
Archive(RCSB-PDB/MSD-EBI
/PDBj)
Native XML-DB
PDBMLplus
PDBMLplusF
download(FTP)
FTP server
Internet
DDBJSwisProt/UniProt
PIR/GenBank/KEGG/GDB/ProTherm/EzCatDB
EBI/CSA/CATRES
Function/Source
Information
Get/Input Tools
CATRESData
AnnotationData
AddInformation
Filtering &Recostructing
PDBMLplus
PDBMLplusF
xPSSS
Manual inputfrom literatures
Primary Citation DB with PDF files
![Page 30: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/30.jpg)
Browser
Primary Citation DatabaseOnly Internal Usages in PDBj
Web input tool
18,814 PDF files have been collected.
![Page 31: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/31.jpg)
Protein Molecular Surface Database, eF-site(Kinoshita & Nakamura)
Protein Dynamics Database, ProMode(Wako & Endo)
Development of other Databases and Services
BioMagResBank-NMR experimental data(Akutsu, Harano & Nakatani)
Search for Similar Surface,eF-seek (Kinoshita & Nakamura)
Electron Microscopy Navigator, EM-Navi (Suzuki)
Encyclopedia of Protein Structures, eProtS(Kinjyo, Kudo, & Ito)
![Page 32: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/32.jpg)
Protein Globe
(Kinjo, A. R. & Standley, D. M.)
Standley, D. M. et al., Brief. Bioinfo. (2008) 9, 276-285.
![Page 33: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/33.jpg)
Protein GlobeBy Akira Kinjo & Daron Standley
http://www.pdbj.org/Globe/
Standley, D. M. et al., Brief. Bioinfo. (2008) 9, 276-285.
![Page 34: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/34.jpg)
All-α
All-β
α/β
![Page 35: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/35.jpg)
eF-site/eF-surf/eF-seek
(Kinoshita, K. & Nakamura, H.)
Kinoshita, K. et al., Nucl. Acids Res. (2007) 35, W398-W402. Kinoshita, K. & Nakamura, H., Protein Sci (2005) 14, 711-718. Kinoshita, K. & Nakamura, H., Bioinformatics (2004) 20, 1329-1330.
![Page 36: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/36.jpg)
eF-site database: http://ef-site.hgc.jp
Almost all PDB entries are calculated.Individual subunits are calculated..Each model for NMR structure is calculated.
![Page 37: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/37.jpg)
Molecular surface and electrostatic potential
Connolly surface(Molecular surface)
Dielectric constant: 80.0
Dielectic constant: 2.0
Charges:AMBER partial chargesGrid size:1.0Å
Ionic strength: 0.1 M
Probe sphere Solvent Accessible Surface
Protein core
Re-entrant surface
![Page 38: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/38.jpg)
What can we see from molecular surface?
[example] Myb proto-oncogene protein
DNA-boundDNA-unbound DNA-bound
![Page 39: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/39.jpg)
eF-site IDPID_ModelID-ChainID
– example: 1a1t_3-AModelID is ignored, when no ModelID
– example: 1tup-CAlphabetic Chain IDs for multiple chains
– example: 1tup-ABCEFLink to individual surfaces
– For each eF-site ID• http://ef-site.hgc.jp/eF-
site/servlet/Summary?entry_id=1tup-EF– For each PDB-ID
• http://ef-site.hgc.jp/eF-site/servlet/Search?pdb=1tup
![Page 40: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/40.jpg)
Summary Page for each Entry
Surface Browsing with jV
Download of each data file
Link to other DBs
![Page 41: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/41.jpg)
Structure Page for surface and structure browsing
![Page 42: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/42.jpg)
Structure based function prediction
Functional site database:Local structure of functional site of proteins
similarity search
Goal– To predict a molecular
function of proteins from their 3D structures
Approach– To search for similar
structures against the functional site database (local structure)
Structural information– Molecular surface
generated by Connolly’s algorithm
– Electrostatic potential obtained by solving Poisson-Boltzmann equations numerically -0.1 +0.1(V)
Function unknown protein
![Page 43: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/43.jpg)
Prediction of Ligand Binding Sites: eF-seekhttp://ef-site.hgc.jp/eF-seek
Prediction of Functional sites by similarity search for eF-siteSearch for representative ligand binding sites
For the uploaded PDB-formatted file, the putative functional sites are predicted, and the assumed complex structures will be replied.
![Page 44: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/44.jpg)
ProMode
(Wako, H. & Endo, S.)
Wako et al., Bioinformatics (2004) 20, 2035-2043.
![Page 45: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/45.jpg)
Database of Normal Mode Analysis of Proteinshttp://promode.socs.waseda.ac.jp/
![Page 46: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/46.jpg)
![Page 47: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/47.jpg)
Command window of jV.
A protein structure vibrating in a given normal mode can be observed (animation displayed by jV and Chime viewer).
Dynamic domains (blue and red regions) are defined for each normal mode.
![Page 48: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/48.jpg)
Dynamic domains (blue and red regions) are defined for each normal mode.
A protein structure vibrating in a given normal mode can be observed (animation displayed by jV and Chime viewer).
![Page 49: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/49.jpg)
Time average properties obtained by the normal mode analysis are shown.
Fluctuation of atoms
Fluctuation of dihedral angles
Correlations between fluctuations of atoms.Red: atom pairs with a strong positive correlationBlue: atom pairs with a strong negative correlation
![Page 50: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/50.jpg)
Example of tetramerFluctuation of atoms
Internal (green) and external (blue) motions of each subunit are shown for oligomer data
New!
![Page 51: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/51.jpg)
EM Navigator
(Suzuki, H.)
![Page 52: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/52.jpg)
What’s EM Navigator?What’s EM Navigator?EM Navigator is • web site for browsing 3D electron microscopy (3D-EM) data
URL: http://emnavi.protein.osaka-u.ac.jp/• based on data from EM Data Bank (EMDB) and Protein Data Bank (PDB)• for non-specialists, beginners, and experts in 3D-EM or structural / molecular biology.
Top page with “Movie Slots” and text-search box
![Page 53: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/53.jpg)
![Page 54: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/54.jpg)
Enjoy viewing 3D structuresEnjoy viewing 3D structures
Interactive structure viewer (jV / Jmol) on Detail page(Data: PDB-ID-1GRU, requires Java Runtime Environment)
Interactive movie player on Movie page(Data: EMDB-ID-1508, requires Adobe Flash Player)
![Page 55: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/55.jpg)
Enter into detailsEnter into details
Detail page for EMDB data (ID: 1261)
Table page to view details of multiple data
Detail page for PDB data (ID: 2J37)
![Page 56: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/56.jpg)
Search, view, and enjoy 3D-EM data !
![Page 57: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/57.jpg)
SeSAWSequence-derived Structure Alignment Weights
for identifying functional sites
• A way of comparing sequence and structure similarities between proteins
• Structural similarities measured using ASH structural alignment program
• Sequence similarities measured using position specific scoring matrices (PSSMs) from psiBLAST
(Standley, D. M.)Standley, D. M. et al., PROTEINS (2008) 72, 1333-1351.
![Page 58: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/58.jpg)
arg 20
1
exp( ( / ) ){ }alignN
T et ASH Blosum Blosum PSSM PSSMm
m
S S d d w S w S=
⎡ ⎤= + − +⎣ ⎦∑
Score for strucutural similarity Blosum62 score Score from PSSM values
dm: distance between the Cα atom pairs in the aligned structures. do: 4A
Identification of Protein Families/Superfamilies
ROC curve
Pfam familySCOP/CATH Superfamily
Confidence Measures
argT etS
TP/
(TP+
FP)
Pfam family
SCOP/CATH Superfamily
Standley, D. M. et al., PROTEINS (2008) 72, 1333-1351.
![Page 59: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/59.jpg)
Example: Hypothetical protein TTHA1568 fromThermus thermophilus 2czl
Co-crystalized withtartaric acid
![Page 60: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/60.jpg)
2czl
![Page 61: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/61.jpg)
2czlA Results
SG Targets
His BindingGlu Binding
Lys/His Binding
SG TargetsGlu Binding
![Page 62: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/62.jpg)
Good match to 2czl: 1ii5, a glutamate-binding protein
2czlA Family: DUF191 1ii5A Family: SBP_bac_3 STarg: 57
![Page 63: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/63.jpg)
2czl and 1ii5 have common binding site
Tartaric acidGlutamate
G82
![Page 64: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/64.jpg)
eProtSEncyclopedia of Protein Structures
(Wiki-eProtS)
(Kudo, T. & Kinjo, A. R.)
![Page 65: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/65.jpg)
Encyclopedia of Protein Structures (Wiki-eProtS)
http://eprots.pdbj.org/
![Page 66: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/66.jpg)
Introduction and request for writing articles of Encyclopedia of Protein Structures (Wiki-eProtS)
Protein Data Bank (PDB)52,535 entries
•select proteins•annotate for the general audience(in English and Japanese)
eProtS322 entries
(at Aug 20,2008)
What’s Encyclopedia of Protein Structures (eProtS) ?
To enlighten and feedback the accomplishment of structural biology to the general public...
![Page 67: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/67.jpg)
Example (α-amylase)
Protein nameSpeciesBiological context
Structure description
Links to PDBj (xPSSS, jV)
Referencesoriginal paper,links to other database,author, and translator
![Page 68: EMBO workshop, 26 Sept. 2008 Tutorials for PDBj Search Tools · xPSSS (xml-based Protein Structure Search Service) PDBML PDBMLplus Web server XSLT processor downloader Loader Archive](https://reader030.vdocument.in/reader030/viewer/2022040420/5e0492755b31bd3da055a7b1/html5/thumbnails/68.jpg)
MembersHead: Haruki NakamuraGroup for PDB Database Curation:Atsushi Nakagawa, Takanori MatsuuraReiko Igarashi, Yumiko Kengaku, Kanna Matsuura,Mayumi Inoue, Chen Minyu
Group for Development of New Tools and Services:Daron M. Standley, Akira R. Kinjo, Hirofumi Suzuki,Reiko Yamashita, Takahiro Kudou, Yukiko Shimizu
Group for NMR Database (BMRB-PDBj):Toshimichi Fujiwara, Hideo Akutsu, Eiichi Nakatani, Yoko Harano
Other Collaborators:Kengo Kinoshita (IMS, Univ. Tokyo), Hiroyuki Toh (MIB, Kyushu Univ.), Hiroshi Wako (Waseda Univ.),Nobutoshi Ito (Tokyo Med. Dent. Univ. )
Secretary:Chisa Kamada