Revision as of 17:53, 24 February 2008

back to the DAS workshop page

SPICE

There are 2 main display modes in SPICE. As a single protein structure browser and as a multiple protein structure alignment viewer.

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 hydrophobicity 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.