Difference between revisions of "Homology based structure prediction (Phenylketonuria)"
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=== Modeller === |
=== Modeller === |
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<figure id="mod_1j8u"> |
<figure id="mod_1j8u"> |
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| − | [[File:Modeller 2pah 1j8u.png|thumb|left|'''<caption>'''Structure of target 2pah (green) and template 1j8u (purple) superimposed. For the creation of the superimpsed |
+ | [[File:Modeller 2pah 1j8u.png|thumb|left|'''<caption>'''Structure of target 2pah (green) and template 1j8u (purple) superimposed. For the creation of the superimpsed structure <code>modeller</code> was used.</caption>]] </figure> |
| − | + | The LGA-RMSD of 1j8u is 0.73 and has a sequence identity of 100% to 2pah, for what reason we also modelled 2phm (xr id="mod_2phm"/>) with a LGA-RMSD of 0.88 and sequence identity of 89.7%. |
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<figure id="mod_2phm"> |
<figure id="mod_2phm"> |
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| − | [[File:Modeller_2pah_2phm.png|thumb|left|'''<caption>'''Structure of target 2pah (green) and template |
+ | [[File:Modeller_2pah_2phm.png|thumb|left|'''<caption>'''Structure of target 2pah (green) and template 2phm(purple) superimposed. For the creation of the superimpsed structure <code>modeller</code> was used.</caption>]] </figure> |
<figure id="mod_3luy"> |
<figure id="mod_3luy"> |
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| − | [[File:Modeller_2pah_3luy.png|thumb|left|'''<caption>'''Structure of target 2pah (green) and template 3luy (purple) superimposed. For the creation of the superimpsed |
+ | [[File:Modeller_2pah_3luy.png|thumb|left|'''<caption>'''Structure of target 2pah (green) and template 3luy (purple) superimposed. For the creation of the superimpsed structure <code>modeller</code> was used.</caption>]] </figure> |
| + | 3luy has a LGA-RMSD of 3.30 and a sequence identity of 22%. |
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Revision as of 16:56, 5 June 2013
Contents
Summary
...
Model calculation
Lab journal
...
Modeller
<figure id="mod_1j8u">
</figure>
The LGA-RMSD of 1j8u is 0.73 and has a sequence identity of 100% to 2pah, for what 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">
</figure>
<figure id="mod_3luy">
</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>
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
...
References
<references/>
