Gaucher Disease: Task 05 - Lab Journal

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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 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)
2XWD_A 91.51 505
2NSX_A 92.53 497
2NT1_A 92.53 497
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
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
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?


TODO: execution scripts


We executed Swiss-Model online using the 'Automatic Modelling Mode'. In the advanced options, the specific template was specified.


We also used iTasser from the web-server. In "Option I" a specific template was specified.

RMSD and GDT-score

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

TMscore <model> <native>


We visualized all created models with Pymol. For this we aligned each model with the reference structures, 1OGS_A and 2V3E_B, and calculated the RMSD between the corresponding C_alpha atoms like in task 4:

align <native> and resi 1-497 and name ca, <model> and resi <from>-<to> and name ca

where "native" is the reference structure (1OGS_A or 2V3E_B) and "model" is the name of the model, "from" is its first residue and "to" its last residue.