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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

MSD motifwww.ebi.ac.uk/msd-srv/msdmotif

Structure Annotation

and

Function Assignment with MSDmotif

PDB: 1gci

small motifs
Small motifs

Alpha-Beta Motif

Nest

ST staple

11 motifs in total

Prof James Milner-White

small motif stats
Small motif stats

Occurrence of amino-acids

Correlation of side chain charge

small motifs viewing
Small motifs viewing

Ligands

Catalytic sites

ProSite

Small motifs

“Group” menu item contains a list of presented in a PDB entry sites and motifs

search
, search

PDB:1gci

Ideal for short loops search

search continue11
, search - continue

PDB:1gci

Subtilases family

PDB:1f5p

Globins family

search vs sequence search
, 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

3d motif research
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

3d motif research continue
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

pattern search
Pattern search

ZN binding pattern: CXXCXXXFXXXXXLXXHXXXH

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

helper application for multiple sequences alignment19
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

sequence hits 3d alignment
Sequence hits 3D alignment

2 hits with less than 25% sequence identity

Fragments alignment

Chains alignment

secondary structure patterns
Secondary structure patterns

Strand – turn – Strand

2-3 residues gap

Glycosylation pattern N{P}[ST]{P}

Where N binds sugar: Man or Nag

msd motif

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

msdmotif as web service
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

xml query example
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>

extending efamily xml
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

msd motif28
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
msdmotif future development
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