Difference between revisions of "Lab Journal - Task 5 (PAH)"

From Bioinformatikpedia
(Modeller)
(Modeller)
Line 2: Line 2:
 
=== Modeller ===
 
=== Modeller ===
 
To use Modeller we follow the [https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Using_Modeller_for_TASK_4 tutorial] written by the students 2011.
 
To use Modeller we follow the [https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Using_Modeller_for_TASK_4 tutorial] written by the students 2011.
*First the target sequence must be provided into PIR-format:
+
*First the target sequence must be provided into PIR-format (2pah has one Lysine at the end and therefore is one aa longer than P00439):
 
<code>
 
<code>
>P1;P00439<br>
+
>P1;2pah<br>
sequence:P00439:::::::0.00: 0.00<br>
+
sequence:2pah:::::::0.00: 0.00<br>
 
MSTAVLENPGLGRKLSDFGQETSYIEDNCNQNGAISLIFSLKEEVGALAKVLRLFEENDV<br>
 
MSTAVLENPGLGRKLSDFGQETSYIEDNCNQNGAISLIFSLKEEVGALAKVLRLFEENDV<br>
 
NLTHIESRPSRLKKDEYEFFTHLDKRSLPALTNIIKILRHDIGATVHELSRDKKKDTVPW<br>
 
NLTHIESRPSRLKKDEYEFFTHLDKRSLPALTNIIKILRHDIGATVHELSRDKKKDTVPW<br>
Line 13: Line 13:
 
QFSQEIGLASLGAPDEYIEKLATIYWFTVEFGLCKQGDSIKAYGAGLLSSFGELQYCLSE<br>
 
QFSQEIGLASLGAPDEYIEKLATIYWFTVEFGLCKQGDSIKAYGAGLLSSFGELQYCLSE<br>
 
KPKLLPLELEKTAIQNYTVTEFQPLYYVAESFNDAKEKVRNFAATIPRPFSVRYDPYTQR<br>
 
KPKLLPLELEKTAIQNYTVTEFQPLYYVAESFNDAKEKVRNFAATIPRPFSVRYDPYTQR<br>
  +
IEVLDNTQQLKILADSINSEIGILCSALQKIK*
IEVLDNTQQLKILADSINSEIGILCSALQKI*
 
 
</code>
 
</code>
   

Revision as of 11:44, 5 June 2013

Model calculation

Modeller

To use Modeller we follow the tutorial written by the students 2011.

  • First the target sequence must be provided into PIR-format (2pah has one Lysine at the end and therefore is one aa longer than P00439):

>P1;2pah
sequence:2pah:::::::0.00: 0.00
MSTAVLENPGLGRKLSDFGQETSYIEDNCNQNGAISLIFSLKEEVGALAKVLRLFEENDV
NLTHIESRPSRLKKDEYEFFTHLDKRSLPALTNIIKILRHDIGATVHELSRDKKKDTVPW
FPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARRKQFADIAYNYRHGQPIPRVEYM
EEEKKTWGTVFKTLKSLYKTHACYEYNHIFPLLEKYCGFHEDNIPQLEDVSQFLQTCTGF
RLRPVAGLLSSRDFLGGLAFRVFHCTQYIRHGSKPMYTPEPDICHELLGHVPLFSDRSFA
QFSQEIGLASLGAPDEYIEKLATIYWFTVEFGLCKQGDSIKAYGAGLLSSFGELQYCLSE
KPKLLPLELEKTAIQNYTVTEFQPLYYVAESFNDAKEKVRNFAATIPRPFSVRYDPYTQR
IEVLDNTQQLKILADSINSEIGILCSALQKIK*

Swissmodel

iTasser

Model evaluation