Difference between revisions of "Gaucher Disease: Task 05 - Lab Journal"

From Bioinformatikpedia
(iTasser)
(RMSD and GDT-score)
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===RMSD and GDT-score===
 
===RMSD and GDT-score===
[http://zhanglab.ccmb.med.umich.edu/TM-score/ TM-score zhanglab]
+
We used the [http://zhanglab.ccmb.med.umich.edu/TM-score/ TM-score tool from Zhang lab] to calculate the GDT-score and RMSD. Execution:
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TMscore <model> <native>
   
 
===Pymol===
 
===Pymol===

Revision as of 12:46, 2 September 2013

This page is still under construction

Calculation of models

Structures set

We assembled the following structures in task 4, now we divide them into two groups: at > 60% and at < 30% sequence identity to our template protein, P04062 (536 aa long). PIDE was calculated as follows:

  • first we aligned the two fasta sequences from PDB with ClustalW
  • then calculated the PIDE (pairwise sequence identity) using SIAS with default options

Selected structures for single-template modelling are written in bold.

Homologous structures to P04062
PDB ID PIDE with target (%) Length (aa)
High PIDE
2XWD_A 91.51 505
2NSX_A 92.53 497
2NT1_A 92.53 497
Low PIDE
2GEP_A 10.74 497
2F7K_A 8.95 327
2QGU 5.59 211
2ISB_A 5.59 192
2DJF_A 3.17 119
2DJF_B 2.98 164
2DJF_C 4.47 69

As the PIDE with P04062 in the low-PIDE group we have selected in task 4 is too low and 10.74% PIDE with 2GEP_A was not enough for Swiss-Model to align the sequences (with BLAST or HHsearch), we looked again at the found hit list in task 2 (HHblits, 2 iterations against Uniprot20 followed by one iteration against pdb_full with E-value cutoff 10E-10). The set of structures finally used is:


Homologous structures to P04062
PDB ID PIDE of alignment with target (%) Length (aa) Aligned columns (aa) Query coverage
High PIDE
3KE0_A 100 497 496 41-536
2XWD_A 100 505 497 40-536
2WKL_A 100 497 496 41-536
2NSX_A 100 497 496 41-536
Low PIDE
2WNW_A 29 447 440 75-534
1VFF_A 22 423 98 151-228
3II1_A 20 535 84 452-514

TODO: brief execution explanation?

Modeller

TODO: execution scripts

Swiss-Model

iTasser

RMSD and GDT-score

We used the TM-score tool from Zhang lab to calculate the GDT-score and RMSD. Execution:

TMscore <model> <native>

Pymol

We visualized all created models with Pymol. For this we aligned each model with the reference structure, 1OGS, and calculated the RMSD between the corresponding C_alpha atoms like in task 4:

align 1ogs_A and resi 1-497 and name ca, model and resi from-to and name ca

where "model" is the name of the model, "from" its first residue and "to" its last residue.