Difference between revisions of "Homology based structure predictions BCKDHA"

From Bioinformatikpedia
(→‎iTasser)
(→‎SWISS-MODEL)
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|2r8o_A || [http://swissmodel.expasy.org/workspace/index.php?userid=e.reisinger@gmx.net&key=914f97bf1dca95ba1aecce9f58c6dadf&func=workspace_modelling&prjid=P000005 2r8o_A]
  
|2r8o_A || [http://swissmodel.expasy.org/workspace/index.php?userid=e.reisinger@gmx.net&key=914f97bf1dca95ba1aecce9f58c6dadf&func=workspace_modelling&prjid=P000005 2r8o_A]
 
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'''Prediction for 2bfd_A'''<br>
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TARGET 51 KPQFPGAS AEFIDKLEFI QPNVISGIPI YRVMDRQGQI INPSEDPHLP
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2bfdA 6 kpqfpgas aefidklefi qpnvisgipi yrvmdrqgqi inpsedphlp
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TARGET sss ss s
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2bfdA sss ss s
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TARGET 99 KEKVLKLYKS MTLLNTMDRI LYESQRQGRI SFYMTNYGEE GTHVGSAAAL
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2bfdA 54 kekvlklyks mtllntmdri lyesqrqgri sfymtnygee gthvgsaaal
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TARGET hhhhhhhhhh hhhhhhhhhh hhhhhhh h hhhhhhhh
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2bfdA hhhhhhhhhh hhhhhhhhhh hhhhhhh h hhhhhhhh
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TARGET 149 DNTDLVFGQY REAGVLMYRD YPLELFMAQC YGNISDLGKG RQMPVHYGCK
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2bfdA 104 dntdlvfgqa reagvlmyrd yplelfmaqc ygnisdlgkg rqmpvhygck
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TARGET sss hhhhh hhhhhhhh h
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2bfdA sss hhhhhh hhhhhhhh h
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TARGET 199 ERHFVTISSP LATQIPQAVG AAYAAKRANA NRVVICYFGE GAASEGDAHA
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2bfdA 154 erhfvtissp latqipqavg aayaakrana nrvvicyfge gaasegdaha
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TARGET hhhhhhh hhhhhhhh ssssssss hhh hhhh
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2bfdA hhhhhhh hhhhhhhh ssssssss hhh hhhh
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TARGET 249 GFNFAATLEC PIIFFCRNNG YAISTPTSEQ YRGDGIAARG PGYGIMSIRV
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2bfdA 204 gfnfaatlec piiffcrnng yaistptseq yrgdgiaarg pgygimsirv
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TARGET hhhhhhhh ssssssss hhhh hhh sssss
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2bfdA hhhhhhhh ssssssss hhhh hhh sssss
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TARGET 299 DGNDVFAVYN ATKEARRRAV AENQPFLIEA MTYRIGHHST SDDSSAYRSV
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2bfdA 254 dgndvfavyn atkearrrav aenqpfliea mtyrig---- ----------
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TARGET ss hhhhhh hhhhhhhhhh hh sssss ss
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2bfdA ss hhhhhh hhhhhhhhhh hh sssss ss
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TARGET 349 DEVNYWDKQD HPISRLRHYL LSQGWWDEEQ EKAWRKQSRR KVMEAFEQAE
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2bfdA 292 -------std hpisrlrhyl lsqgwwdeeq ekawrkqsrr kvmeafeqae
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TARGET hhhhhhhh h hhh hhhhhhhhhh hhhhhhhhhh
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2bfdA hhhhhhhh h hhh hhhhhhhhhh hhhhhhhhhh
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TARGET 399 RKPKPNPNLL FSDVYQEMPA QLRKQQESLA RHLQTYGEHY PLDHFDK
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2bfdA 354 rkpkpnpnll fsdvyqempa qlrkqqesla rhlqtygehy pldhfdk-
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TARGET h h hhhhhhhhhh hhhhh
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2bfdA h h hhhhhhhhhh hhhhh
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<code>
   
 
=== iTasser ===
  
=== iTasser ===

Revision as of 19:44, 7 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:
-2bfd_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, -1w85_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:
-2bfd_A
< 40% sequence identity (ideally go towards 20%) :
-2r8o_A

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]

To run modeller with more than one target we use the targets:
-1DTW:A 95%
-2BFE:A 94%
-2BFB:A 99%
-2bfd:A 99%
-3m49:A 31%
-1gpu:A 22%
-2o1x:A 18%

Protocol 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

SWISS-MODEL server:

ID link
2bfd_A 2bfd_A
2r8o_A 2r8o_A


Prediction for 2bfd_A

TARGET    51      KPQFPGAS AEFIDKLEFI QPNVISGIPI YRVMDRQGQI INPSEDPHLP
2bfdA     6       kpqfpgas aefidklefi qpnvisgipi yrvmdrqgqi inpsedphlp
                                                                     
TARGET                                             sss   ss s         
2bfdA                                              sss   ss s         


TARGET    99    KEKVLKLYKS MTLLNTMDRI LYESQRQGRI SFYMTNYGEE GTHVGSAAAL
2bfdA     54    kekvlklyks mtllntmdri lyesqrqgri sfymtnygee gthvgsaaal
                                                                     
TARGET          hhhhhhhhhh hhhhhhhhhh hhhhhhh             h hhhhhhhh  
2bfdA           hhhhhhhhhh hhhhhhhhhh hhhhhhh             h hhhhhhhh  


TARGET    149   DNTDLVFGQY REAGVLMYRD YPLELFMAQC YGNISDLGKG RQMPVHYGCK
2bfdA     104   dntdlvfgqa reagvlmyrd yplelfmaqc ygnisdlgkg rqmpvhygck
                                                                     
TARGET              sss       hhhhh     hhhhhhhh h                    
2bfdA               sss       hhhhhh    hhhhhhhh h                    


TARGET    199   ERHFVTISSP LATQIPQAVG AAYAAKRANA NRVVICYFGE GAASEGDAHA
2bfdA     154   erhfvtissp latqipqavg aayaakrana nrvvicyfge gaasegdaha
                                                                     
TARGET                        hhhhhhh hhhhhhhh     ssssssss hhh   hhhh
2bfdA                         hhhhhhh hhhhhhhh     ssssssss hhh   hhhh


TARGET    249   GFNFAATLEC PIIFFCRNNG YAISTPTSEQ YRGDGIAARG PGYGIMSIRV
2bfdA     204   gfnfaatlec piiffcrnng yaistptseq yrgdgiaarg pgygimsirv
                                                                     
TARGET          hhhhhhhh   ssssssss                    hhhh hhh  sssss
2bfdA           hhhhhhhh   ssssssss                    hhhh hhh  sssss


TARGET    299   DGNDVFAVYN ATKEARRRAV AENQPFLIEA MTYRIGHHST SDDSSAYRSV
2bfdA     254   dgndvfavyn atkearrrav aenqpfliea mtyrig---- ----------
                                                                     
TARGET          ss  hhhhhh hhhhhhhhhh hh   sssss ss                   
2bfdA           ss  hhhhhh hhhhhhhhhh hh   sssss ss                   


TARGET    349   DEVNYWDKQD HPISRLRHYL LSQGWWDEEQ EKAWRKQSRR KVMEAFEQAE
2bfdA     292   -------std hpisrlrhyl lsqgwwdeeq ekawrkqsrr kvmeafeqae
                                                                      
TARGET                      hhhhhhhh    h    hhh hhhhhhhhhh hhhhhhhhhh
2bfdA                       hhhhhhhh    h    hhh hhhhhhhhhh hhhhhhhhhh


TARGET    399   RKPKPNPNLL FSDVYQEMPA QLRKQQESLA RHLQTYGEHY PLDHFDK   
2bfdA     354   rkpkpnpnll fsdvyqempa qlrkqqesla rhlqtygehy pldhfdk-  
                                                                     
TARGET          h                   h hhhhhhhhhh hhhhh                
2bfdA           h                   h hhhhhhhhhh hhhhh

iTasser

2bfd_A
2bfd_A


Prediction for 2bfd_A


This prediction is based on several templates fount by iTasser itself.

Protocol Swissmodel

2.Evaluation of models

As we want to compare the predicted models to the existing PDB entry we need the PDB file for 1U5B. Here only chain A is important, as the sequence for chain A was used to create the models. Therefore chain B has to be removed from the PDB file. Herefore we used a program names ExtractChains.pl provided by <ref>http://www.rosettacommons.org/guide/PDB+Manipulation+Scripts</ref>.

Swissmodel

Numeric evaluation

QMEAN4 global scores

QMEANscore4

2bfd_A 2r8o_A
0.67 0.271


QMEAN Z-Score

2bfd_A 2r8o_A
-1.604 -6.943
Z-Score plot1 2bfd_A
Z-Score plot1 2r8o_A
Z-Score plot2 2bfd_A
Z-Score plot2 2r8o_A


Score components

2bfd_A 2r8o_A
score components 2bfd_A
score components 2r8o_A


Local scores

2bfd_A 2r8o_A
Coloring by residue error 2bfd_A
Coloring by residue error 2r8o_A
Residue error plot 2bfd_A
Residue error plot 2r8o_A


Global scores: QMEAN4:

2bfd_A 2r8o_A
Scoring function term Raw score Z-score Raw score Z-score
C_beta interaction energy -162.66 0.54 -47.91 -1.49
All-atom pairwise energy -10811.93 0.35 -2558.65 -1.98
Solvation energy -27.04 -1.02 10.53 -4.08
Torsion angle energy -75.78 -1.45 18.95 -4.99
QMEAN4 score 0.670 -1.60 0.271 -6.94


Local Model Quality Estimation

2bfd_A 2r8o_A
Local Model Quality Estimation 2bfd_A
Local Model Quality Estimation 2r8o_A

iTasser

Numeric evaluation

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