Difference between revisions of "Gaucher Disease: Task 03 - Sequence-based predictions"

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Revision as of 17:50, 26 May 2013

Secondary Structure

TODO: What features are predicted? Discuss the results for your protein and the example proteins. Using the predictions, what could you learn about your protein and the example proteins? Compare to the available knowledge in UniProt, PDB, DisProt, OPM, PDBTM, Pfam...

Disorder

Transmembrane Helices

Comparison of TMH for Q9YDF8
Prediction Assignment
Memsat SVN Polyphobius OPM PDMTM
# of TMH 6 7
TMH Topology 43-59
72-90
101-118
128-143
163-184
221-245
42-60
68-88
108-129
137-157
163-184
196-213
224-244
N-terminal cytoplasmic extracellular
C-terminal cytoplasmic cytoplasmic
Signal peptide blub blub

Signal Peptides

GO Terms

Discussion

Other available methods

Prediction of Tool Information
secondary structure GOR http://gor.bb.iastate.edu/
disorder DISOPRED2 http://bioinf.cs.ucl.ac.uk/psipred/
transmembrane helices MEMSAT3 http://bioinf.cs.ucl.ac.uk/psipred/
TMHMM http://www.cbs.dtu.dk/services/TMHMM/
signal peptides
GO terms

What else can/is be predicted from protein sequence alone

  • Fold recognition (profile based pGenTHREADER and rapid GenTHREADER)
  • Fold domain recognition (pDomTHREADER)
  • Protein domain prediction (DomPred)
  • Homology modelling (BioSerf v2.0)
  • Function prediction (eukaryotic function: FFPred v2.0)
  • Prediction of TM topology and helix packing (SVM-based MEMPACK)

http://bioinf.cs.ucl.ac.uk/psipred/

Which predictions can be improved considerably by structure-based approaches