Homology based structure prediction (Phenylketonuria)

Summary

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Model calculation

Lab journal

Single template modeling

Modeller

</figure> </figure> </figure>

Structure of target 2pah (green) and template 1j8u (purple) superimposed. For the creation of the superimposed structure Modeller was used.

Structure of target 2pah (green) and template 2phm(purple) superimposed. For the creation of the superimposed structure Modeller was used.

Structure of target 2pah (green) and template 3luy (purple) superimposed. For the creation of the superimposed structure Modeller was used.

<figure id="mod_1j8u">

<figure id="mod_2phm">

<figure id="mod_3luy">

The LGA-RMSD of 1j8u is 0.73 and has a sequence identity of 100% to 2pah, for that reason we also modelled 2phm (<xr id="mod_2phm"/>) with a LGA-RMSD of 0.88 and sequence identity of 89.7%.

3luy has a LGA-RMSD of 3.30 and a sequence identity of 22%.

Swissmodel

SwissModel ... <ref name="swissmodel"> Konstantin Arnold, Lorenza Bordoli, Jürgen Kopp and Torsten Schwede (2006): "The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling". Bioinformatics Vol.22(2): 195-201. doi:10.1093/bioinformatics/bti770 </ref> <figure id="swiss_1j8u">

Structure of target 2pah (green) and template 1j8u (purple) superimposed. For the creation of the superimposed structure Swissmodell was used.

</figure>

<figure id="swiss_3luy">

Structure of target 2pah (green) and template 3luy (purple) superimposed. For the creation of the superimposed structure Swissmodell was used.

</figure>

iTasser

iTasser... <ref name="itasser"> Yang Zhang (2008): "[zhanglab.ccmb.med.umich.edu/papers/2008_2.pdf I-TASSER server for protein 3D structure prediction]". BMC Bioinformatics Vol.9: 40. doi:10.1186/1471-2105-9-40 </ref>

Model evaluation

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References

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