1. EMBL-EBI Adel Golovin MSDsite The project is funded by the European Commission as the TEMBLOR, contract-no. QLRI-CT- 2001-00015 under the RTD programme "Quality of Life and Management of Living Resources"

2. EMBL-EBI MSDsite

3. EMBL-EBI  Many protein (and some nucleic acids) structures have evolved as a framework for an active site – where chemistry takes place.  The active site is critical for the understanding the action of proteins and their role within the cell mechanism.  The function, of these macromolecules can best be studied by detailed 3-dimensional knowledge of these active sites.  Because the active site is a local 3D environment. Introduction

4. EMBL-EBI  The 3D / 1D position that defines the protein function  disparate amino acids on the 1D sequence  A localized volume in 3D  Where chemistry/binding happens. Ligand environment

5. EMBL-EBI  The MSD site database contains local structural information around all the bound ligands within the PDB  All proteins deposited to the PDB are checked for ligand(s). These are HETATM & non-protein/non-nucleic- acid/non-water residues.  Interactions are stored within the DB  The bound ligand coordinates & associated information  The ligand environment (i.e. any residue that interacts)  The interaction types between the ligand and environment.  All sequences are checked for the registered ProSite patterns and matches are stored in the DB  Fast algorithm for a pattern search is embedded into the DB MSD site database

6. EMBL-EBI  Sites are defined as a ligand environment when a ligand is presented.  Sequence motifs matching is applied for site definition independently from ligands.  ProSite sites http://www.expasy.org/prosite  Catalytic sites atlas http://www.ebi.ac.uk/thornton-srv/databases/CSA/  Merops active sites http://merops.sanger.ac.uk/ Site definitions

7. EMBL-EBI  Covalent Bonds  Coordinate bonds  Hydrogen bonds  Planes  Non-bonding  Electrostatics  Di-Sulphide bonds  Geometry (distance, angles..) PHE O N S ASPASP VALVAL Ligand environment analysis Site DB Structure DB Environment

8. EMBL-EBI  Define search by ligand  Define search by sequence motif (pattern)  Define search by metal site geometry  Define search by environment  has same environment  has similar environment Possible site searches

9. EMBL-EBI Structure Protein Ligand Define target: equal/like Filter by PDB header: equal/like Environment exact/sub set Search criteria Sequence motif Metal site geometry Search options

10. EMBL-EBI Statistics search Interactive Charts Ligand binding Environment binding Atomic bonds Sequence pattern binding

11. EMBL-EBI Search method Search front form Statistics search Result list Detail views

12. EMBL-EBI MSDsite interface Filters Query editor

13. EMBL-EBI HIS|SER:S/H>C2.0 HIS.NE2:S/S>C2.0 HIS.[N]/T>C2.0 Drawing Complex queries secondary structure Distance cut-offs Bond type Side/main chain Query generation

14. EMBL-EBI Search service aims  Form a site search criteria  Provide a hit list Visualize the found sites  XML technology (xpath,..) to search an XML corresponding to a PDB entry from the hit list.

15. EMBL-EBI Example Pattern is defined as : HIS-any-HIS-GLU

16. EMBL-EBI Hit List Help

17. EMBL-EBI AstexViewer  @MSD-EBI : Default PDB viewer: chemical/x-pdb. RasMol script viewer: application/x-rasmol. Hit List Visualization tools

18. EMBL-EBI Searched site visualization AstexViewer[tm] Groups menu

19. EMBL-EBI Goto Site details Hit List Link to Details Bound molecules form Sequence from Atomic bonds

20. EMBL-EBI Detail forms header Ligand binding statistics Links to the other views of the same PDB entry Switch on/off undefined bonds

21. EMBL-EBI Show site Sequence form search for PDB entries with the same hetero ID and similar environment

22. EMBL-EBI Bound molecules form Ligands that match a search creteria Environment statistics

23. EMBL-EBI Environment binding statistics Filters HIS HIS HIS Trnasformed to HIS>C HIS>C HIS>I

24. EMBL-EBI Bound molecules form Bonds details on atomic level

25. EMBL-EBI Atomic bonds view Atomic bonds statistics

26. EMBL-EBI Atomic bonds statistics

27. EMBL-EBI Detail forms header Ligand binding statistics

28. EMBL-EBI Ligand binding statistics Distribution type Filters

29. EMBL-EBI Ligand binding statistics – distribution by whole environment

30. EMBL-EBI Pattern binding statistics Pattern: H-x-H-E

31. EMBL-EBI 3D aligned views  Superimposed by ligand  Superimposed by environment  Superimposed by pattern  Superimposed by active site

32. EMBL-EBI 3D aligned views

33. EMBL-EBI 3D aligned views – EBI- AstexViewer[tm]

34. EMBL-EBI

35.  DB of active sites has been generated  Application server has been developed  The DB can be searched  Based on properties of the ligand environment  Based on properties of the ligand  Based on properties of structure and sequence of the parent protein Summary

36. EMBL-EBI Data generated by data mining of common packing of chemical groups is being added. (Proteins S.F.G, 49:510-528, T.J.Oldfield). This information contains about 2000 sites, 1/3 with ligands. Future sites