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MSD motif www.ebi.ac.uk/msd-srv/msdmotif

MSD motif www.ebi.ac.uk/msd-srv/msdmotif. Structure Annotation and Function Assignment with MSDmotif. PDB: 1gci. MSDmotif front options. Small motifs. Alpha-Beta Motif. Nest. ST staple. 11 motifs in total Prof James Milner-White. Small motif stats. Occurrence of amino-acids.

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MSD motif www.ebi.ac.uk/msd-srv/msdmotif

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

  2. MSDmotif front options

  3. Small motifs Alpha-Beta Motif Nest ST staple 11 motifs in total Prof James Milner-White

  4. Small motif stats Occurrence of amino-acids Correlation of side chain charge

  5. Small motif stats

  6. Small motifs – hit list from stats

  7. Small motifs – 3D alignment ST-staple

  8. 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. , search PDB:1gci Ideal for short loops search

  10. , search - continue

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

  12. , 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. 3D motif research Asx turn 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

  14. 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. Pattern search ZN binding pattern: CXXCXXXFXXXXXLXXHXXXH

  16. Pattern hits 3D alignment

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

  18. 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. 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. Sequence hits 3D alignment 2 hits with less than 25% sequence identity Fragments alignment Chains alignment

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

  22. Secondary structure patterns - continue

  23. Secondary structure patterns - continue

  24. 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. MSDmotif as web service XML respond as eFamily XML MSDmotif server XML query 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. XML query example Task: Find PDB entries where a ligand is capping a helix and at the same time binds its N-termini. <?xml version="1.0" encoding="UTF-8" ?> <!DOCTYPE query …>- <query useUndefinedBonds="yes" phipsiDeviation="10" eValue="auto">- <declaration> <ligand>x l</ligand> <ss>H h</ss> </declaration> <interaction>l.[O]<->h.first.N=H</interaction> <interaction>l.[O]<->h.last.N<3.5</interaction> </query>

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

  28. 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. 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

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