Homology based structure predictions BCKDHA
Contents
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%.
These are the templates we will work with:
> 60% sequence identity:
-1w85_A -> P21873
< 40% sequence identity (ideally go towards 20%) :
-2r8o_A -> P27302
Modeller
MODELLER is used for homology or comparative modeling of protein three-dimensional structures.It calculates a model containing all non-hydrogen atoms. There are also many other tasks provided by MODELLER like de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc.[1]
A tutorial is provided on [2] and on [3]
SWISS-MODEL
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
SWISS-MODEL server:
| ID | link |
|---|---|
| 1w85_A | 1w85_A |
| 2r8o_A | 2r8o_A |
iTasser
| 1w85_A |
| 1w85_A |
2.Evaluation of models
Numeric evaluation
QMEAN4 global scores
QMEANscore4
| 1w85_A | 2r8o_A |
|---|---|
| 0.596 | 0.271 |
QMEAN Z-Score
| 1w85_A | 2r8o_A |
|---|---|
| -2.872 | -6.943 |
Score components
| 1w85_A | 2r8o_A |
|---|---|
Local scores
| 1w85_A | 2r8o_A |
|---|---|
Global scores: QMEAN4:
| 1w85_A | 2r8o_A | |||
|---|---|---|---|---|
| Scoring function term | Raw score | Z-score | Raw score | Z-score |
| C_beta interaction energy | -152.10 | 0.11 | -47.91 | -1.49 |
| All-atom pairwise energy | -9145.04 | -0.55 | -2558.65 | -1.98 |
| Solvation energy | -14.56 | -2.14 | 10.53 | -4.08 |
| Torsion angle energy | -57.90 | -2.03 | 18.95 | -4.99 |
| QMEAN4 score | 0.596 | -2.87 | 0.271 | -6.94 |
Local Model Quality Estimation
| 1w85_A | 2r8o_A |
|---|---|
