Difference between revisions of "Gaucher Disease: Task 03 - Sequence-based predictions"
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Revision as of 17:50, 26 May 2013
Contents
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 |
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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/