Latest revision as of 11:31, 26 February 2008

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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.

Find the hsa35pep DAS track in the Ensembl peptide display.

Map the exon structure onto 3D.

Map the nsSNPs onto 3D.

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.

SPICE & histogram style data

examples for how to display histogram style plots in SPICE can be see from here: http://www.efamily.org.uk/software/dasclients/spice/histogram.shtml

SPICE homepage

Just for completeness, you can of course also launch SPICE via its homepage at http://www.efamily.org.uk/software/dasclients/spice/

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.