Homology based structure prediction (Phenylketonuria)

Summary

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Model calculation

Lab journal

Single template modeling

Modeller

<figure id="mod_1j8u">

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

</figure>

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%. <figure id="mod_2phm">

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

</figure>

<figure id="mod_3luy">

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

</figure>

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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