View source for Homology based structure predictions BCKDHA

== 1.Calculation of models  ==
To find similar structures to BCKDHA we ran HHsearch: <br>
hhsearch -i query -d database -o output<br><br>

It found the following 10 hits in the pdb70 database.

{| border="1"
!No
!Hit
!Prob
!E-value
!P-value
!Score
!SS
!Cols
!Query HMM
!Template HMM
!Identity
|-
| 1 || 2bfd_A 2-oxoisovalerate dehydr ||  1.0   ||    1   ||    1 || 791.3  || 0.0 || 400  ||  1-400  ||   1-400 (400)||99%
|-
| 2 || 1qs0_A 2-oxoisovalerate dehydr ||  1.0   ||    1   ||    1 || 571.5  || 0.0 || 349  || 32-382  ||  52-407 (407)||39%
|-
| 3 || 1w85_A Pyruvate dehydrogenase  ||  1.0   ||    1   ||    1 || 530.8  || 0.0 || 356  ||  8-382  ||   6-362 (368) ||34%
|-
| 4 || 1umd_A E1-alpha, 2-OXO acid de || 1.0    ||   1    ||   1 || 521.8 ||  0.0 || 351 ||  34-386 ||   16-367 (367)||37%
|-
| 5 || 2ozl_A PDHE1-A type I, pyruvat ||  1.0   ||    1   ||    1 || 482.7 ||  0.0 || 331 ||  46-380 ||   25-356 (365)||27%
|-
| 6 || 3l84_A Transketolase; TKT, str ||  1.0    ||   1   ||    1 ||  85.4 ||  0.0 || 133 || 161-297 ||  113-252 (632)||21%
|-
| 7 || 2r8o_A Transketolase 1, TK 1; ||   1.0   ||    1   ||    1 ||  74.5 ||  0.0 || 121 ||  161-285 ||  113-245 (669)||33%
|-
| 8 || 2o1x_A 1-deoxy-D-xylulose-5-ph ||  1.0   ||    1  ||     1 ||  74.2 ||  0.0  ||127 || 161-287 ||  122-254 (629)||18%
|-
| 9 || 1gpu_A Transketolase; transfer ||  1.0   ||    1  ||     1  || 74.2  || 0.0 || 140 || 161-302  || 115-265 (680)||22%
|-
| 10 || 3m49_A Transketolase; alpha-be ||  1.0   ||    1  ||     1 ||  68.8  || 0.0 || 121 || 161-285 ||  139-271 (690)||31%
|}

 > 60% sequence identity:
   -1w85_A<br>
 > 40% sequence identity: <br><br>
 < 40% sequence identity (ideally go towards 20%) :
   -1qs0_A, 1umd_A, 1w85_A, 2r8o_A, 3m49_A, 2ozl_A, 1gpu_A, 3l84_A, 2o1x_A 
<br>
HHSearch has only hits with an identity higher than 60% or lower than 40%. This is why we had to take one hit of our BLAST run.<br>
 >gi|91094507|ref|XP_971663.1|  Score=507 bits (1306), E-value=e-142, Identities=228/397 (57%), Positives=296/397 (74%), Gaps=2/397 (0%)
<br>
These are the templates we will work with:
 > 60% sequence identity:
   -1w85_A  -> P21873<br>
 > 40% sequence identity: 
   -XP_971663.1  -> D6X542<br>
 < 40% sequence identity (ideally go towards 20%) :
   -2r8o_A  -> P27302<br><br>
<br>
=== Modeller ===

=== SWISS-MODEL ===
[[File:WorkplaceSWISSMODEL.jpg | thumb |right | SWISS-MODEL server page]]<br>
To find protein structure homology models SWISS-MODEL can be used. As input it needs a protein sequence or a UniProt AC Code. Optional the template PDB-Id and the chain or a template file can be assigned. 
SWISS-MODEL is a fully automated protein structure homology-modeling server. It is accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer).
<br>
[[http://swissmodel.expasy.org/workspace/index.php?func=modelling_simple1 SWISS-MODEL]]

=== iTasser ===

== 2.Evaluation of models ==

=== Numeric evaluation ===

===== QMEAN4 global scores =====

QMEANscore4
{|border="1"
!1w85_A
|-
|0.596 
|}


QMEAN Z-Score<br>
{|border="1" 
!1w85_A 
|-
| -2.872
|-
|[[File:QMEAN_Zscore_1_1w85_A.png | thumb | Z-Score plot1]]
|-
|[[File:QMEAN_Zscore_2_1w85_A.png | thumb| Z-Score plot2]]
|}

<br>
Score components<br>
{|border="1" 
!1w85_A
|-
|[[File:Score_components_1w85_A.png| thumb |score components]]
|}


===== Local scores =====