Difference between revisions of "Structural Alignments (Phenylketonuria)"
From Bioinformatikpedia
(→Modelling scores) |
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| − | === |
+ | === TopMatch === |
| − | [https://topmatch.services.came.sbg.ac.at/ |
+ | [https://topmatch.services.came.sbg.ac.at/ TopMatch] |
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| SSAP-RMSD || 0.99 || 18.77 || 1.24 || 1.02 || 39.16 || 22.39 || 7.27 |
| SSAP-RMSD || 0.99 || 18.77 || 1.24 || 1.02 || 39.16 || 22.39 || 7.27 |
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+ | | TopMatch-Er ||0.60 || 1.98 || 0.81 || 0.63 || 1.21 || 1.12 || 3.25 |
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| CE-RMSD || 0.65 || 5.13 || 0.95 || 0.68 || 4.06 || 4.68 || 5.92 |
| CE-RMSD || 0.65 || 5.13 || 0.95 || 0.68 || 4.06 || 4.68 || 5.92 |
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| − | <center><small>'''<caption>'''Root-mean-square deviation/error in Ångström for the four protein structure alignment predictors LGA, SSAP, |
+ | <center><small>'''<caption>'''Root-mean-square deviation/error in Ångström for the four protein structure alignment predictors LGA, SSAP, TopMatch and CE.</caption></small></center> |
</figtable> |
</figtable> |
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Revision as of 10:17, 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
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/>
