Difference between revisions of "Homology based structure predictions BCKDHA"

From Bioinformatikpedia
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===== Global scores: QMEAN4: =====
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{|border="1"
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!
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!colspan="2" | 1w85_A
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!Scoring function term
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!Raw score
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|C_beta interaction energy || -152.10 || 0.11
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|All-atom pairwise energy ||-9145.04 || -0.55
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|Solvation energy ||-14.56 || -2.14
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|Torsion angle energy || -57.90 || -2.03
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|QMEAN4 score || 0.596 || -2.87
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===== Local Model Quality Estimation =====
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!1w85_A
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|[[File:Local_Model_Quality_Estimation_1w85.png | thumb | 1w85_A]]
 
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Revision as of 21:45, 5 June 2011

1.Calculation of models

To find similar structures to BCKDHA we ran HHsearch:
hhsearch -i query -d database -o output

It found the following 10 hits in the pdb70 database.

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

> 40% sequence identity: 


< 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


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.

>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%)


These are the templates we will work with: 

> 60% sequence identity:
  -1w85_A  -> P21873

> 40% sequence identity: 
  -XP_971663.1  -> D6X542

< 40% sequence identity (ideally go towards 20%) :
  -2r8o_A  -> P27302


Modeller

SWISS-MODEL

SWISS-MODEL server page


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).
[SWISS-MODEL]

iTasser

2.Evaluation of models

Numeric evaluation

QMEAN4 global scores

QMEANscore4

1w85_A
0.596


QMEAN Z-Score

1w85_A
-2.872
Z-Score plot1
Z-Score plot2


Score components

1w85_A
score components


Local scores
1w85_A
Coloring by residue error
Residue error plot


Global scores: QMEAN4:
1w85_A
Scoring function term Raw score Z-score
C_beta interaction energy -152.10 0.11
All-atom pairwise energy -9145.04 -0.55
Solvation energy -14.56 -2.14
Torsion angle energy -57.90 -2.03
QMEAN4 score 0.596 -2.87


Local Model Quality Estimation
1w85_A
1w85_A
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