Difference between revisions of "Homology modeling fallback data"

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<div id="BIO">
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<div style="padding: 5px; background: #D3D8E8;  border:solid 1px #AAAAAA;">
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<div class="b1">
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Please remember: if you use information from this page as a '''fallback for technical problems with the assignment''', you must document this in your submission. State what you tried, what didn't work and only then use the data from here.
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Homology Modeling<br />
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<span style="font-size: 70%">Fallback Data</span>
 
</div>
 
</div>
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Here are results from a homology modeling exercise using SwissModel, as a '''fallback for technical problems with the assignment''' i.e network problems or other issues with the program or input data.
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==Target sequence==
 
==Target sequence==
  
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>MBP1_CHAGL XP_001224558:33..108
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This is just one of the reference species' sequences - I chose <code>Mbp1_SCHPO</code> because it is the most distantly related to ''saccharomyces cerevisiae''.
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HVMRRREDNWINATHILKAAGFDKPARTRILERDVQKDVHEKIQGGYGKY
 
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QGTWIPLEQGRALAQRNNIYDRLRPIF
 
  
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==FASTA formatted alignment==
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>MBP1_SCHPO NP_593032 23..96
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IKGVSVMRRRRDSWLNATQILKVADFDKPQRTRVLERQVQIGAHEKVQGGYGKYQGTWVPFQRGVDLATK
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YKV
  
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>1MB1 sequence from coordinates 3..100
 
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NQIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTR
 
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ILEKEVLKETHEKVQGGFGKYQGTWVPLNIAKQLAEKFSVYDQLKPLF                   
 
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>MBP1_CHAGL XP_001224558:33..108
 
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---------------------HVMRRREDNWINATHILKAAGFDKPARTR
 
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ILERDVQKDVHEKIQGGYGKYQGTWIPLEQGRALAQRNNIYDRLRPIF
 
  
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==FASTA formatted target-template alignment==
  
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This uses the 1BM8 PDB file as template.
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>1BM8_A
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QIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRI
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LEKEVLKETHEKVQGGFGKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDF
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>Mbp1_SCHPO 2-100 NP_593032
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AVHVAVYSGVEVYECFIKGVSVMRRRRDSWLNATQILKVADFDKPQRTRV
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LERQVQIGAHEKVQGGYGKYQGTWVPFQRGVDLATKYKVDGIMSPILSL
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There are no gaps and the sequences align over the whole length. If the sequences were of different length, the shorter one would have to be padded with gap characters: <code>"-"</code>.
  
 
==SwissModel response==
 
==SwissModel response==
  
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Four e-mails are sent by SwissModel after submission of the modeling request. Two of the received files are ''welcome'' and ''help'' messages. Two other e-mail messages conatin the program output and the model.
 
  
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:*[[Assignment_5_SwissModel_Results| SwissModel '''Program Output''']]
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Explanation of the output is found [http://swissmodel.expasy.org/workspace/index.php?func=special_help '''in the SwissModel Help page'''].
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:*[[Assignment_5_SwissModel_Model| SwissModel attached '''Model Coordinates''']]
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[[Image:ModelledRange.png|frame|none|Graphical comparison of template and target sequence to emphasize which regions have been modelled. Given the good, full-length alignment, SwissModel had no problem modeling the entire protein.]]
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==LGA superposition==
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[[Image:QMeanScore.png|frame|none|Model QMEAN score vs. expected QMean scores of protein structures, as a function of domain size. The model (red cross) is within the lower 2 sigma range in quality for its size.]]
  
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The resulting output produced by the LGA server for the 1DUX_ABC and 1MB1 superposition consists of two parts: the superposition report explains which residues were matched and what their RMSD after superposition was. The coordinates contain the rotated coordinates of the entire 1DUX file superimposed on 1MB1. In order to use this for as RasMol, the following manual edits were performed.
 
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:#LGA created several <code>END  </code> records in the middle of the file. These prevent the following lines to be read in. They were simply deleted. Since the protein chans of the Mbp1 and Elk-1 domains are closely superimposed, RasMol tries to draw multiple bonds between  the residues that have close contacts. This was addressed by bracketing the chains in <code>MODEL</code> and <code>ENDMDEL</code>, which prevents bonds between being drawn.
 
  
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:*[[Assignment_5_LGA_Results| '''LGA superposition report''']]
 
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:*[[Assignment_5_1DUX_1MB1| '''1DUX_1MB1 Coordinates''']]
 
  
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==Protein-DNA complex model==
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[[Image:ColoringByScore.jpg|frame|none|Cartoon view of the model, colored by QMEAN scores]]
  
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The DNA coordinates (chain A and B) from the LGA superimposed coordinate file were copied, and pasted into the SwissModel coordinate file, thus generating a homology model of a Protein / DNA complex.
 
  
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:*[[Assignment_5_Model_DNA| '''Model/DNA complex Coordinates''']]
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The target-template alignment:
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TARGET    1      AVHVAVYS GVEVYECFIK GVSVMRRRRD SWLNATQILK VADFDKPQRT
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1bm8A    4      qiysarys gvdvyefihs tgsimkrkkd dwvnathilk aanfakakrt
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TARGET            sssssss  ssssssss  sssssss    ssshhhhh h    hhhhh
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1bm8A            sssssss  ssssssss  sssssss    ssshhhhh h    hhhhh
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TARGET    49    RVLERQVQIG AHEKVQGGYG KYQGTWVPFQ RGVDLATKYK VDGIMSPILS
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1bm8A    52    rilekevlke thekvqggfg kyqgtwvpln iakqlaekfs vydqlkplfd
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TARGET          hhhhhh      sss        ssss hh hhhhhhhh    hh  hhhh
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1bm8A          hhhhhh      sss        ssss hh hhhhhhhh    hh  hhhh
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TARGET    99    L                                                   
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1bm8A    102  f-                                                   
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TARGET                                                               
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1bm8A                         
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[[Image:ModelQualityEstimation.png|frame|none|Local quality estimation: '''ANOLEA''' and '''QMEAN''' scores as graphical output]]
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==Model data==
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* [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/SCHPO_model.pdb SCHPO_model.pdb]: MBP1_SCHPO APSES domain model coordinates
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* [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/Local_energy_profile.csv Local_energy_profile.csv]: Energy scores for the MBP1_SCHPO APSES domain model coordinates
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&nbsp;
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[[Category:Bioinformatics]]
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</div>

Latest revision as of 02:41, 5 November 2012

Homology Modeling
Fallback Data


Here are results from a homology modeling exercise using SwissModel, as a fallback for technical problems with the assignment i.e network problems or other issues with the program or input data.

   


Target sequence

This is just one of the reference species' sequences - I chose Mbp1_SCHPO because it is the most distantly related to saccharomyces cerevisiae. 

>MBP1_SCHPO NP_593032 23..96
IKGVSVMRRRRDSWLNATQILKVADFDKPQRTRVLERQVQIGAHEKVQGGYGKYQGTWVPFQRGVDLATK
YKV


FASTA formatted target-template alignment

This uses the 1BM8 PDB file as template. 

>1BM8_A
QIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRI
LEKEVLKETHEKVQGGFGKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDF
>Mbp1_SCHPO 2-100 NP_593032
AVHVAVYSGVEVYECFIKGVSVMRRRRDSWLNATQILKVADFDKPQRTRV
LERQVQIGAHEKVQGGYGKYQGTWVPFQRGVDLATKYKVDGIMSPILSL

There are no gaps and the sequences align over the whole length. If the sequences were of different length, the shorter one would have to be padded with gap characters: "-".

SwissModel response

Explanation of the output is found in the SwissModel Help page.

Graphical comparison of template and target sequence to emphasize which regions have been modelled. Given the good, full-length alignment, SwissModel had no problem modeling the entire protein.


Model QMEAN score vs. expected QMean scores of protein structures, as a function of domain size. The model (red cross) is within the lower 2 sigma range in quality for its size.


Cartoon view of the model, colored by QMEAN scores


The target-template alignment: 

TARGET    1       AVHVAVYS GVEVYECFIK GVSVMRRRRD SWLNATQILK VADFDKPQRT
1bm8A     4       qiysarys gvdvyefihs tgsimkrkkd dwvnathilk aanfakakrt
                                                                     
TARGET            sssssss   ssssssss   sssssss     ssshhhhh h    hhhhh
1bm8A             sssssss   ssssssss   sssssss     ssshhhhh h    hhhhh


TARGET    49    RVLERQVQIG AHEKVQGGYG KYQGTWVPFQ RGVDLATKYK VDGIMSPILS
1bm8A     52    rilekevlke thekvqggfg kyqgtwvpln iakqlaekfs vydqlkplfd
                                                                     
TARGET          hhhhhh       sss         ssss hh hhhhhhhh    hh   hhhh
1bm8A           hhhhhh       sss         ssss hh hhhhhhhh    hh   hhhh


TARGET    99    L                                                     
1bm8A     102   f-                                                    
                                                                     
TARGET                                                                
1bm8A
Local quality estimation: ANOLEA and QMEAN scores as graphical output

Model data


 

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