Protein Database in Europe Deposition Validation Search and

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

worldwide Protein Data Bank (ww. PDB) • 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 (mm. CIF) and XML are also available.

Protein Databank in Europe (PDBe) group • Is one of the four sites around the world that where 3 D 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.

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

Depositions and Curation Deposition via Auto. Dep 4 (http: //www. ebi. ac. uk/pdbe-xdep/autodep) Closely collaborate with the other ww. PDB members for a single unified archive. . Depositions via EMDEP (http: //www. ebi. ac. uk/pdbe-emdep/emdep) Depositions started June 2002

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

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

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 PDBe Relational Database Improved Query Functionality Crystallographers Biologists Time Effort Usefulness Usage Programmers Bioinformaticians

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

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

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

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: ü "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

PDBe. View

Search result: The Atlas page

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

Astex. Viewer™: 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 Astex. Viewer™ from Astex Technology Limited and modified under licence by the PDBe group

PDBe. Chem Ligand Database

PDBe. Motif What is the environment around alpha-D-mannose and beta-D-mannose?

PDBe. Motif What binds ASP HIS LYS ?

PDBe. Motif How does ATP generally interact with LYS in all structures ?

PDBe. Analysis Assess Quality of a Structure Bond Angles Ramachandran Plot Bond Distances

PDBe. Pisa What assembly can my structure have ?

PDBe. Fold 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 ?

Chem. Search Sub-structure based search of a million chemicals

PDBe. Analysis/PDBe. Validate Online PDB validation

PDBe. Status 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.

PDBechem ligand data Sequence Mapping, SIFTS Electron Density Visualisation Astex. Viewer PDBe. Pro, PDBelite Active sites Linking to Domain data, e. Family PISA biological assemblies Fold matching Surface Matching