1. EBI is an Outstation of the European Molecular Biology Laboratory. Protein Database in Europe Gaurav Sahni, Ph.D. Deposition, Validation, Search and Analysis Services

2. worldwide Protein Data Bank (wwPDB) Consists of four sites RCSB (USA), PDB-j (Japan) BMRB (USA) and PDBe. Single repository of macromolecular structures. Started in 1971 and now ~56,000 entries, adding ~200 new entries/week. Deposited by experimentalists and contents is freely available. The format of the archive is flat-files with fixed line format, although an improved flat-file format (mmCIF) and XML are also available.

3. Protein Databank in Europe (PDBe) group Is one of the four sites around the world that where 3D structures may be deposited. Provides stable and clean repository of macromolecular structure data. Has services that allow users to access, search and retrieve structural data from a single web access point.

4. EBI is an Outstation of the European Molecular Biology Laboratory. PDBe Tasks Deposition and Validation Database design and implementation Retrieve data Analysis tools & Services

5. Deposition via AutoDep4 (http://www.ebi.ac.uk/msd-srv/autodep4/) Closely collaborate with the other wwPDB members for a single unified archive.. Depostions via EMDEP (http://www.ebi.ac.uk/msd-srv/emdep/) Depositions started June 2002 Depositions and Curation

6. Validation of Structures Authentication of source That the protein is from human and not rabbit, for example ! Authentication of structure Comparison of structure against raw data. Geometry and Stereochemistry. Provide results back to depositor. Validation of correct methodology used Whether X-Ray, NMR or EM. Conformity to standards Follows PDB format specifications Error checks Consistency checks - to identify simple typos Homo sapiens and not Homo sapien (single human?). Outlier detection - to identify suspect records

7. EBI is an Outstation of the European Molecular Biology Laboratory. PDBe Tasks Deposition site Database design and implementation Retrieve data Analysis tools & Services

8. Disadvantages of Flat files… Macromolecular structures are very complex. Existing PDB format is incapable of fully describing few existing structures also. Format is not readily extensible, to cope, for example, with structural genomics data. Historical archive is non-uniform and poorly populated. Search and retrieval of flat files is difficult and/or inaccurate.

9. Uniform Data Improved Query Functionality Time Effort Usefulness Usage CrystallographersBiologists ProgrammersBioinformaticians PDBe Relational Database

10. EBI is an Outstation of the European Molecular Biology Laboratory. PDBe Tasks Deposition site Database design and implementation Retrieve data Analysis tools & Services

11. Some Implementation Issues  The PDBe database is large and complex:  ~56,000 PDB entries  Cross-referenced against SwissProt, PubMed etc.  Making data accessible without adding additional complexity.  Tools for different categories of end-user  Novice user - biobar  Experienced user - PDBelite  Expert user – PDBepro

12. biobar A toolbar search application for Mozilla/Netscape or firefox browsers http://biobar.mozdev.org/ Simple and quick retrieval of data from PDBe and 45 other Databases

13. PDBelite A simple form-based query system to search the PDBe Databases

14. PDBelite Search Results

15. Features of Search Interface Strengths: simple, easy to use form allows multiple search fields to be combined relatively fast, despite performing quite complex SQL queries Weaknesses: not exposing the power of a relational database limited logical operators between search fields: "name" AND "title" AND "keyword“  "name" OR "title" OR "keyword“  ( "name" OR "title" ) AND NOT "keyword" the search form is defined by the authors of the search system, not the author of a query

16. PDBepro A java-based flexible graphical search interface for advanced searching

17. Complex searches User have comprehensive control of their query Applet provide a dynamic form, as compared to a static HTML form: choose the fields to be searched specify the relationships between search fields choose the result fields and how results are presented perform “complex” sub-queries e.g. SSM, FASTA PDBepro uses an applet for constructing queries and a server to execute them The user describes their query entirely graphically, including logical operations such as AND, OR and NOT

18. Search result: The Atlas page

19. EBI is an Outstation of the European Molecular Biology Laboratory. PDBe Tasks Deposition site Database design and implementation Retrieve data Analysis tools & Services

20. AstexViewer™: Visualization@PDBe View structures as wireframe, backbone or ribbons Built-in sequence viewer Calculate and display surfaces Various display options: Ramachandran plots Distance matrix B-factors Based on the AstexViewer™ from Astex Technology Limited and modified under licence by the PDBe group

21. PDBeChem Ligand Database

22. What is the environment around alpha-D-mannose and beta-D-mannose? PDBeSite

23. What binds ASP ASP HIS LYS ? PDBeSite

24. How does ATP generally interact with LYS in all structures ? PDBeSite

25. Assess Quality of a Structure Ramachandran Plot Bond Distances Bond Angles PDBeAnalysis

26. PDBePisa What assembly can my structure have ?

27. PDBeFold Discover unknown relationships… Are there any structures in the PDB that are similar to mine? What SCOP and/or CATH family could my structure belong to ? Can I get some idea about the possible function of my protein based on similarity with others based on structural similarity ? Mutiple alignment of many of my structures ?

28. PDBe provides… Clean biological data Integrated data A single web access point Query interfaces for different users (Beginner, Occasional or expert). Interconnected views of the data relating structure, sequence, text & experimental details.

29. PISA biological assemblies PDBechem ligand data Electron Density Visualisation AstexViewer PDBePro, PDBelite Fold matching Surface Matching Active sites Linking to Domain data, eFamily Sequence Mapping, SIFTS