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

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 ~61,000 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.

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.

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

Deposition via AutoDep4 ( Closely collaborate with the other wwPDB members for a single unified archive.. Depositions via EMDEP ( Depositions started June 2002 Depositions and Curation

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

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

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.

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

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

Some Implementation Issues  The PDBe database is large and complex:  ~61,000 PDB entries  Cross-referenced against SwissProt, PubMed etc.  Making data accessible without adding additional complexity.  Tools for different categories of end-user  Simple – biobar  Intermediate - PDBelite  Advanced – PDBepro  New - PDBeView

biobar A toolbar search application for Mozilla/Netscape or firefox browsers Simple and quick retrieval of data from PDBe and 45 other Databases

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

PDBelite Search Results

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

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

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

PDBeView

Search result: The Atlas page

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

AstexViewer™: 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

PDBeChem Ligand Database

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

What binds ASP ASP HIS LYS ? PDBeSite

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

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

PDBePisa What assembly can my structure have ?

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 ?

ChemSearch Sub-structure based search of a million chemicals

PDBeAnalysis/PDBeValidate Online PDB validation

PDBeStatus PDB Deposition status search

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.

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