@*~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. *@