Difference between revisions of "Structural Alignments (Phenylketonuria)"
From Bioinformatikpedia
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=== SAP or CE === |
=== SAP or CE === |
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| − | [http://mathbio.nimr.mrc.ac.uk/wiki/SAP SAP?] |
+ | [http://mathbio.nimr.mrc.ac.uk/wiki/SAP SAP?] ->Error!<br> |
| − | -> |
+ | -><br> |
[http://source.rcsb.org/jfatcatserver/ceHome.jsp CE] |
[http://source.rcsb.org/jfatcatserver/ceHome.jsp CE] |
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[http://www.rcsb.org/pdb/workbench/workbench.do CE-PDB] |
[http://www.rcsb.org/pdb/workbench/workbench.do CE-PDB] |
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Revision as of 10:39, 30 May 2013
Contents
Summary
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Explore structural alignments
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Dataset generation
Our protein has the CATH Code: 1.10.800.10 (Phenylalanine Hydroxylase)
- reference structure of PAH: 2PAH (96,41% identity)
- identical sequence with filled binding site: 1LRM (--> pdb entry: looked at 3D structure and saw a filled binding site, two ligands: FE and HBI)
- identical sequence with unfilled binding site: not found anyone
- low sequence identity: 3LUY (32,2% - no pdb ID under 30%)
- high sequence identity: pdb ID: 2PHM (89,7%)
- CAT: 1J8U (CATH Code: 1.10.800.10) - there is no other category than 1.10.800.10 for CAT
- CA: 2B5U (CATH Code: 1.10.287.620)
- C: 3BQO (CATH Code: 1.25.40.210)
- other CATH category: 1V8H (CATH Code: 2.60.40.10)
Pymol
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LGA
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SSAP / CATHEDRAL (used by CATH)
SSAP ...
TopMatch
TopMatch ...
SAP or CE
SAP? ->Error!
->
CE
CE-PDB
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Modelling scores
<figtable id="rmsd">
| RMSD results | |||||||
|---|---|---|---|---|---|---|---|
| Method | 1lrm | 3luy | 2phm | 1j8u | 2b5u | 3bqo | 1vh8 |
| LGA-RMSD | 0.81 | 3.30 | 0.88 | 0.73 | 3.07 | 3.59 | 3.42 |
| SSAP-RMSD | 0.99 | 18.77 | 1.24 | 1.02 | 39.16 | 22.39 | 7.27 |
| TopMatch-Er | 0.60 | 1.98 | 0.81 | 0.63 | 1.21 | 1.12 | 3.25 |
| CE-RMSD | 0.65 | 5.13 | 0.95 | 0.68 | 4.06 | 4.68 | 5.92 |
</figtable>
Evaluate sequence alignments
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References
<references/>
