Difference between revisions of "Homology based structure prediction (Phenylketonuria)"
From Bioinformatikpedia
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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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+ | === Modeller === |
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+ | ==== Single template modeling ==== |
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|<figure id="mod_1j8u">[[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> |
|<figure id="mod_1j8u">[[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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| + | ==== Multiple alignments ==== |
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| − | ==== Swissmodel ==== |
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| + | === Swissmodel === |
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[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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| − | + | === iTasser === |
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[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 === |
=== Multiple Alignments === |
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Revision as of 17:28, 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
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>
Multiple Alignments
Model evaluation
...
References
<references/>
