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Calculation of models
Lab journal
We created two single target models of our protein sequence, P04062: one with a high sequence identity target,2XWD_A, and one with a low sequence identity target, 2WNW_A, with each one of the three tools: Modeller, Swiss-Model and iTasser.
For Modeller we additionally executed multiple target modeling mode. In the multiple target modeling mode, Modeller first aligns the user selected templates, then adds the target to the MSA, which is finally used for modeling. We tried the following template combinations:
- close homologues (> 60% sequence identity): all four (3KE0_A, 2XWD_A, 2WKL_A and 2NSX_A)
- distant homologues (< 30% sequence identity): all three (2WNW_A, 1VFF_A and 3II1_A)
- close and distant homologues: 2XWD_A and 2WNW_A
Evaluation of models
Modeller
- Pymol alignment of models of P04062 computed by Modeller (lime) with the original structure 1OGS, chain A (purple). For the templates, chains A were used.
Model using template 2XWD and malign alignment method. RMSD=0.284 (408 C_alpha atoms pairs).
Model using template 2XWD and salign alignment method. RMSD=0.284 (408 C_alpha atoms pairs).
Model using template 2WNW and malign alignment method. RMSD=1.217 (340 C_alpha atoms pairs).
Model using template 2WNW and salign alignment method. RMSD=1.523 (337 C_alpha atoms pairs).
Model using templates with high sequence identity: 3KE0, 2XWD, 2WKL and 2NSX and salign alignment method. RMSD=0.272 (439 C_alpha atoms pairs).
Model using templates with low sequence identity: 2WNW, 1VFF and 3II1 and salign alignment method. RMSD=20.935 (471 C_alpha atoms pairs).
Model using templates with mixed sequence identity: high 2XWD and low 2WNW and salign alignment method. RMSD=0.328 (418 C_alpha atoms pairs).
Swiss-Model
- Pymol alignment of models of P04062 computed by Swiss-Model (lime) with the original structure 1OGS, chain A (purple). For the templates, chains A were used.
Model using template 2XWD. RMSD=0.305 (407 C_alpha atoms pairs).
Model using template 2WNW. RMSD=1.105 (368 C_alpha atoms pairs).
iTasser
- Pymol alignment of models of P04062 computed by iTasser (lime) with the original structure 1OGS, chain A (purple). For the templates, chains A were used.
Model using template 2XWD. Estimated accuracy of Model1: 0.67±0.13 (TM-score), 8.2±4.5Å (RMSD)
Model using template 2WNW. Estimated accuracy of Model1: 0.66±0.13 (TM-score), 8.4±4.5Å (RMSD)