DASworkshop200802:spice
Contents
SPICE
a browser for protein sequences, structures and their annotations
There are various ways to launch SPICE.
Ensembl
The PDB_Spice DAS track in the Ensembl protview and contigviews allows to show protein structure mappings/
e.g. http://www.ensembl.org/Homo_sapiens/protview?peptide=ENSP00000365116
enable the track in this view and click on the track and then again on the protein structure image. This allows you to launch SPICE.
Pfam
SPICE can be easily linked to from external web sites.
Find the protein structure 1cdg in Pfam: http://pfam.sanger.ac.uk/structure?entry=1boh&type=Structure
click on view structure and select SPICE again.
notice how the PFAM track is on top of the UniProt display. map the PFAM domains on the structure.
Do the PFAM domains correspond to what you would consider structural domains?
Find the hydrophobicity DAS source. (in the UniProt display, very much at the bottom) map the Kyle-Doolittle accessibility onto the protein structure.
A multiple structure alignment viewer
CASP 7 results
The CASP 7 - target view allows to launch SPICE in the structure alignment mode
white... solved target.
others: predictions for various targets.
sort predictions by score
switch between sequence based on structure based alignment algorithms.
