Difference between revisions of "Homology based structure prediction (Phenylketonuria)"
From Bioinformatikpedia
(→Multiple alignments) |
(→Multiple alignments) |
||
| Line 24: | Line 24: | ||
{| |
{| |
||
|<figure id="mod_1j8u">[[File:Multiple_2pah_bigger60.png|thumb|left|'''<caption>'''Structure of target 2pah (green) and alignment of templates 1j8u, 2phm, 1qey and 1phz (purple) superimposed. For the creation of the superimposed structure <code>Modeller</code> was used.</caption>]] </figure> |
|<figure id="mod_1j8u">[[File:Multiple_2pah_bigger60.png|thumb|left|'''<caption>'''Structure of target 2pah (green) and alignment of templates 1j8u, 2phm, 1qey and 1phz (purple) superimposed. For the creation of the superimposed structure <code>Modeller</code> was used.</caption>]] </figure> |
||
| − | |<figure id="mod_2phm">[[Multiple_2pah_mixture.png|thumb|left|'''<caption>'''Structure of target 2pah (green) and alignment of templates 1j8u, 2phm, 3luy and 1wyp (purple) superimposed. For the creation of the superimposed structure <code>Modeller</code> was used.</caption>]] </figure> |
+ | |<figure id="mod_2phm">[[File:Multiple_2pah_mixture.png|thumb|left|'''<caption>'''Structure of target 2pah (green) and alignment of templates 1j8u, 2phm, 3luy and 1wyp (purple) superimposed. For the creation of the superimposed structure <code>Modeller</code> was used.</caption>]] </figure> |
|<figure id="mod_3luy">[[File:Multiple 2pah smaller30.png|thumb|left|'''<caption>'''Structure of target 2pah (green) and alignment of templates 3luy, 1wyp, 2v27 and 2qmx (purple) superimposed. For the creation of the superimposed structure <code>Modeller</code> was used.</caption>]] </figure> |
|<figure id="mod_3luy">[[File:Multiple 2pah smaller30.png|thumb|left|'''<caption>'''Structure of target 2pah (green) and alignment of templates 3luy, 1wyp, 2v27 and 2qmx (purple) superimposed. For the creation of the superimposed structure <code>Modeller</code> was used.</caption>]] </figure> |
||
|} |
|} |
||
Revision as of 19:16, 5 June 2013
Contents
Summary
...
Model calculation
Modeller
Single template modeling
</figure> </figure> </figure>| <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%.
...
Multiple alignments
</figure> </figure> </figure>| <figure id="mod_1j8u"> |
| <figure id="mod_2phm"> |
| <figure id="mod_3luy"> |
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> </figure>| <figure id="swiss_1j8u"> |
| <figure id="swiss_3luy"> |
...
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/>
