@*~RSC_HELP_TUTORIAL_BLAST_PDB
Introduction
Protein alignments are more accurate with
3D structures being used for computation.
This tutorial shows how the 3D-structures of a given amino acid sequence is obtained.
The WIKI:Blast service at the EBI will be used to identify similar sequences in the PDB-database.
The protein sequence UNIPROT:SUBT_BACSU will serve as an example. You can download this protein simply by mouse click or use
the dialog HTMLDOC_BUTTON:BUT_C1(DialogFetchSRS)!
Searching for 3D structures
Select the sequence SUBT_BACSU and click the tool-button HTMLDOC_BUTTON:SBUT_3D!.
The dialog identifies similar but not necessarily identical sequences in the 3D database.
HTMLDOC_JCOMPONENT:HTMLDOC_JC_DialogSimilarStructure
When the computation is finished you can click the button in the column "Apply".
Strap will download the protein file and infer the 3D structure to SUBT_BACSU.
Finally the 3D structure is shown.
By clicking into this basic 3D view, the 3D menu-bar is put in place.
It has a black background to be distinguished from the standard menu-bar.
From the 3D menu-bar, sophisticated 3D views can be opened.
Alternatively, the dialog HTMLDOC_BUTTON:BUT_C1(DialogBlast)! can be used. Here the
user can inspect the search result to identify a suitable 3D
model.
*@