PACKAGE:charite.christo.
Introduction
It has been demonstrated in the introduction-tutorial that alignments are more accurate when
3D structure is used for computation.
This tutorial shows how the 3D-structures of a given amino acid sequence is obtained.
The program WIKI:BLAST will be used to identify similar sequences in the PDB-database.
The protein sequence SWISS:SUBT_BACSU will serve as an example.
Retrieving the protein file
At first the protein file "SUBT_BACSU" must be fetched from the Sequence Retrieval System (SRS).
Please open the dialog BUTTON:DialogFetchSRS! and type "SUBT_BACSU" into the text-area of this dialog.
There are several highlight buttons, each referring to a certain string pattern.
"SUBT_BACSU" matches the pattern letters/Digits-underscore-letters/Digits.
When the button BUTTON:"SRS" is pressed the sequence file will be fetched from the server.
The downloaded file is listed in a new result tab (see figure below).
Activate the file and press
BUTTON:FilesFetchedFromServer#BUT_LAB_Load
to load the protein into the alignment pane.
Blasting
Open the dialog BUTTON:DialogBlast!.
Select the protein "SUBT_BACSU" and the BLAST program COMBO:Blaster_ebi_ac_uk and the database COMBO:"pdb ".
Start the BLAST by pressing LABEL:ChButton#BUTTON_GO.
It takes about a minute to get a BLAST result like
...
> PDB:1ST3_ mol:protein length:269 SUBTILISIN BL
Score = 850 (304.3), Expect = 1.4E-85
Identities = 59/274, Positives = 78/274
Q 108 QSVPYGISQIKAPALHSQGYTGSNVKVAVIDSGIDSSHPDLNVRGGASFVPSETNPYQDG 167
QSVP+GIS+++APA H++G TGS VKVAV+D+GI S+HPDLN+RGGASFVP E + QDG
H 2 QSVPWGISRVQAPAAHNRGLTGSGVKVAVLDTGI-STHPDLNIRGGASFVPGEPST-QDG 59
....
> PDB:1TEC_E mol:protein length:279 THERMITASE
Score = 553 (199.7), Expect = 4.1E-54
Identities = 43/280, Positives = 62/280
Q 106 YAQSVPYGISQIKAPALHSQGYTGSNVKVAVIDSGIDSSHPDL--NVRGGASFVPSETNP 163
Y S YG +I+AP GS K+A++D+G+ S+HPDL V GG FV +++ P
H 7 YFSSRQYGPQKIQAPQAWDIA-EGSGAKIAIVDTGVQSNHPDLAGKVVGGWDFVDNDSTP 65
...
Convenient downloading the PDB files
The expression "PDB:1TEC_E" means chain E of PDB entry pdb1tec.
Watch the mouse cursor when you move the mouse over this expression.
If the link is clicked left from the colon the PDB-entry is shown in the Web-browser, but if it is
clicked right from the colon the protein is loaded into
STRAP.
Downloading with the download dialog
If you want to download a large number of PDB-entries listed in some sort of text like a BLAST result, then use the dialog BUTTON:DialogFetchPdb!.