Difference between revisions of "Modeller protocol BCKDHA"

From Bioinformatikpedia
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The TM scores were calculated using the program 'TMScore'<ref>http://zhanglab.ccmb.med.umich.edu/TM-score/</ref>. This program also return a pdb file with superpositioned template and structure in the C-alpha trace, which was used to visualize the modelling results.
 
The TM scores were calculated using the program 'TMScore'<ref>http://zhanglab.ccmb.med.umich.edu/TM-score/</ref>. This program also return a pdb file with superpositioned template and structure in the C-alpha trace, which was used to visualize the modelling results.
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=== Visualization ===
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The created models were visualized using Pymol <ref> http://pymol.org</ref>. The target structure (1U5B, Chain A) and each template were loaded and superpositioned. As the secondary structure elements are best visualized using the 'cartoon' mode, the structures were displayed in cartoon mode by the following commands:
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hide everything, all
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show cartoon, all
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To view two superimposed structures the <code>align</code> command was applied:
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align iTasser_2bfd_mod, 1U5B_chain
   
 
=== References ===
 
=== References ===

Revision as of 15:17, 13 June 2011

Calculation of Models

Modeller

To get Modeller started, we first had to create a few starting files.

For each of our template sequences 2bfd and 2r8o we had to create a pairwise alignment with our target sequence 1u5b. This pairwise alignment should be in the modeller PIR format. To build this alignments we wrote a script which can be also run by modeller. This script bases on an example script located in /apps/modeller9.9/examples/comments.

Modeller takes an py-file which specifies the sequences and alignment file to be used. The model-default.py can be found in /apps/modeller9.9/examples/automodel. Here we changed 'alignment.ali' to 1w85_1u5b.pir, knowns = '1W85' (our first target) and sequence = '1U5B' (out template). The file was saved as model1w85.py (for more information see [1])

Make sure to provide the PDB coordinate files in the folder /atom-files.

Modeller is executed by the following command:

mod9.9 model1w85.py


Modeller can also be called with more than one template. A description how this is done can be found here:[2]

Swissmodel

Swissmodel offers three different modes to model Proteins (automated mode, alignment mode, project mode).

The automated mode uses fully automated modelling and can therefore be only used when the template is very similar to the target.<ref>http://swissmodel.expasy.org/?pid=smd03&uid=&token=</ref>

As an Input for the automated mode, only an amino acid sequence (raw or FASTA format) or the Uniprot AC of the target is required. Optional a template PDB id can be given. Swissmodel automatically selects templates from a Blast run which are suitable due to their E-values if no template is given.



The alignment mode can be used for multiple sequence alignments where at least one PDB structure is known.

'Modelling' Steps:

1. Create an (multiple) alignment of at least the target and the template sequence (Format: FASTA, MSF, CLUSTALW, PFAM and SELEX) We created a multiple alignment using ClustalW<ref>http://www.ebi.ac.uk/Tools/msa/clustalw2/</ref>.

2. Submit the alignment to Swissmodel's alignment mode and make sure it is interpreted correctly

Evaluation

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 only chain A should be present in a PDB file. Herefore we used a program named getFirstChain.pl provided by <ref>http://www.rosettacommons.org/guide/PDB+Manipulation+Scripts</ref>.

RMSD

First we calculated the C_alpha RMSD using a tool called DaliLite <ref>http://www.ebi.ac.uk/Tools/dalilite/index.html</ref> which is provided by EMBL-EBI. Then we also used the command line tool "sap".

TM Score

The TM scores were calculated using the program 'TMScore'<ref>http://zhanglab.ccmb.med.umich.edu/TM-score/</ref>. This program also return a pdb file with superpositioned template and structure in the C-alpha trace, which was used to visualize the modelling results.

Visualization

The created models were visualized using Pymol <ref> http://pymol.org</ref>. The target structure (1U5B, Chain A) and each template were loaded and superpositioned. As the secondary structure elements are best visualized using the 'cartoon' mode, the structures were displayed in cartoon mode by the following commands:

hide everything, all

show cartoon, all


To view two superimposed structures the align command was applied:

align iTasser_2bfd_mod, 1U5B_chain

References

<references />

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