Difference between revisions of "Homology based structure prediction (Phenylketonuria)"
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== Model calculation == |
== Model calculation == |
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[[Lab Journal - Task 5 (PAH) #xxx|Lab journal]] <br> |
[[Lab Journal - Task 5 (PAH) #xxx|Lab journal]] <br> |
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| + | === Single template modeling === |
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| − | ... |
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| + | ==== Modeller ==== |
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| − | === 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 superimposed structure <code>modeller</code> was used.</caption>]] </figure> |
[[File:Modeller 2pah 1j8u.png|thumb|left|'''<caption>'''Structure of target 2pah (green) and template 1j8u (purple) superimposed. For the creation of the superimposed structure <code>modeller</code> was used.</caption>]] </figure> |
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| − | === Swissmodel === |
+ | ==== Swissmodel ==== |
[http://swissmodel.expasy.org/workspace/index.php?func=modelling_simple1&userid=USERID&token=TOKEN SwissModel] ... <ref name="swissmodel"> Konstantin Arnold, Lorenza Bordoli, Jürgen Kopp and Torsten Schwede (2006): "[http://bioinformatics.oxfordjournals.org/content/22/2/195.full The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling]". Bioinformatics Vol.22(2): 195-201. [http://en.wikipedia.org/wiki/Digital_object_identifier doi]:[http://bioinformatics.oxfordjournals.org/content/22/2/195.full 10.1093/bioinformatics/bti770] </ref> |
[http://swissmodel.expasy.org/workspace/index.php?func=modelling_simple1&userid=USERID&token=TOKEN SwissModel] ... <ref name="swissmodel"> Konstantin Arnold, Lorenza Bordoli, Jürgen Kopp and Torsten Schwede (2006): "[http://bioinformatics.oxfordjournals.org/content/22/2/195.full The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling]". Bioinformatics Vol.22(2): 195-201. [http://en.wikipedia.org/wiki/Digital_object_identifier doi]:[http://bioinformatics.oxfordjournals.org/content/22/2/195.full 10.1093/bioinformatics/bti770] </ref> |
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<figure id="swiss_1j8u"> |
<figure id="swiss_1j8u"> |
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| − | === iTasser === |
+ | ==== iTasser ==== |
[http://zhanglab.ccmb.med.umich.edu/I-TASSER/ 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. [http://en.wikipedia.org/wiki/Digital_object_identifier doi]:[http://www.biomedcentral.com/1471-2105/9/40/ 10.1186/1471-2105-9-40] </ref> |
[http://zhanglab.ccmb.med.umich.edu/I-TASSER/ 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. [http://en.wikipedia.org/wiki/Digital_object_identifier doi]:[http://www.biomedcentral.com/1471-2105/9/40/ 10.1186/1471-2105-9-40] </ref> |
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| + | === Multiple Alignments === |
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== Model evaluation == |
== Model evaluation == |
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Revision as of 17:16, 5 June 2013
Contents
Summary
...
Model calculation
Single template modeling
Modeller
<figure id="mod_1j8u">
</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">
</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> <figure id="swiss_1j8u">
</figure>
<figure id="swiss_3luy">
</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>
Multiple Alignments
Model evaluation
...
References
<references/>
