1. EMBL-EBI MSD motif www.ebi.ac.uk/msd-srv/msdmotif PDB: 1gci Structure Annotation and Function Assignment with MSDmotif

2. EMBL-EBI MSDmotif front options

3. EMBL-EBI Small motifs Alpha-Beta MotifNestST staple 11 motifs in total Prof James Milner-White

4. EMBL-EBI Small motif stats Occurrence of amino-acidsCorrelation of side chain charge

5. EMBL-EBI Small motif stats

6. EMBL-EBI Small motifs – hit list from stats

7. EMBL-EBI Small motifs – 3D alignment ST-staple

8. EMBL-EBI Small motifs viewing Ligands Catalytic sites ProSite Small motifs “Group” menu item contains a list of presented in a PDB entry sites and motifs

9. EMBL-EBI ,  search Ideal for short loops search PDB:1gci

10. EMBL-EBI ,  search - continue

11. EMBL-EBI ,  search - continue PDB:1gci Subtilases family PDB:1f5p Globins family

12. EMBL-EBI ,  search vs sequence search Sequences found while search by ,  : Subtilases family NNSIGVL DNTTGVL DNSIGVL Globins family IVDTGSV Blast search for NNSIGVL Diphtheria toxin family SDSIGVL

13. EMBL-EBI 3D motif research PDB 1e4m has the small motif - Asx turn of residues 65-67 (ASP-HIS-GLY), which is found in a loop between two helixes Use phi/psi parameters of these three residues for a search Asx turn

14. EMBL-EBI 3D motif research - continue The sequences from the hit list: LKY QGF DRF AGV RGV DHG MGK DNL HGV ANN TGA QCY LGA NSY Most of these hits were found in loops between helixes

15. EMBL-EBI Pattern search ZN binding pattern: CXXCXXXFXXXXXLXXHXXXH

16. EMBL-EBI Pattern hits 3D alignment

17. EMBL-EBI Sequence search Pseudo multiple sequence alignment (blast output based) Ligand binding residues are marked Normalization of hit list to 50% sequence identity

18. EMBL-EBI Helper application for multiple sequences alignment Blixem as helper browser application for multiple sequences alignment based on blast output Mime-type: application/x-blast Blixem http://www.cgb.ki.se/cgb/groups/sonnhammer/Blixem.html

19. EMBL-EBI Helper application for multiple sequences alignment Jalview as helper browser application for sequences alignment Mime-type: application/x-align http://www.jalview.org/ Alignment of Zinc binding PROSITE patter hits

20. EMBL-EBI Sequence hits 3D alignment 2 hits with less than 25% sequence identity Fragments alignmentChains alignment

21. EMBL-EBI Secondary structure patterns Where N binds sugar: Man or Nag Strand – turn – Strand Glycosylation pattern N{P}[ST]{P} 2-3 residues gap

22. EMBL-EBI Secondary structure patterns - continue

23. EMBL-EBI Secondary structure patterns - continue

24. EMBL-EBI MSD motif Small 3D motifs from J.Milner-White search/view Secondary structure patterns (HTH) search/view , ,  based search/view Ligands and their environment search/view Catalytic sites search/view Blast sequence search/view PROSITE format compliant patterns search/view 3D and sequence multiple alignment Hit list and statistics normalization by SCOP,CATH

25. EMBL-EBI MSDmotif as web service XML query MSDmotif server XML respond as eFamily XML www.eFamily.org.uk Hydrogen bonds , ,  angles Secondary structures + small motifs Secondary structure patterns Sequence patterns Blast sequences Prosite, Catalytic sites, Merops Ligands, fragments, SMILEs Ligand interactions Arithmetic operations XML query

26. EMBL-EBI XML query example Task: Find PDB entries where a ligand is capping a helix and at the same time binds its N-termini. - x l H h l.[O] h.first.N=H l.[O] h.last.N

27. EMBL-EBI Extending eFamily XML Standard ways of extending an XML schema: - extension - restriction - substitution group segment Helix Strand Beta-turn Gamma-turn Alpha-beta-motif Asx-turn ST-turn ST-staple … entry pdb-entry entity Chain Bound-molecule Water-group

28. EMBL-EBI MSD motif www.ebi.ac.uk/msd-srv/msdmotif 32000 PDBs, 25 G disk space on Oracle DB, linear dependency ~ 0.8 M per PDB Web application server with J2EE servlet engine NCBI Blast for sequence search

29. EMBL-EBI MSDmotif future development 3D alignment extension Water interactions Statistical analysis and presentation –Secondary structure patterns –Statistics from MSDmotif hit list –Correlation of different parameters like residues weight, csi/phi/psi angles. Neural network for recognition of complex structure fragments/motifs in a PDB and their function association