Difference between revisions of "Homology modeling fallback data"
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| − | + | Homology Modeling<br /> | |
| + | <span style="font-size: 70%">Fallback Data</span> | ||
</div> | </div> | ||
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| + | Here are results from a homology modeling exercise using SwissModel, as a '''fallback for technical problems with the assignment''' i.e network problems or other issues with the program or input data. | ||
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==FASTA formatted target-template alignment== | ==FASTA formatted target-template alignment== | ||
| − | This uses the | + | This uses the 1BM8 PDB file as template, the sequence was extracted from coordinates using the WhatIf server. |
| − | > | + | >1BM8_A |
| − | + | QIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRI | |
| − | + | LEKEVLKETHEKVQGGFGKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDF | |
| − | > | + | >Mbp1_SCHPO 2-100 NP_593032 |
| − | + | AVHVAVYSGVEVYECFIKGVSVMRRRRDSWLNATQILKVADFDKPQRTRV | |
| − | + | LERQVQIGAHEKVQGGYGKYQGTWVPFQRGVDLATKYKVDGIMSPILSL | |
| + | [TBC once the SwissModel server is back...] | ||
==SwissModel response== | ==SwissModel response== | ||
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* [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/MBP1_SCHPO_APSES_MODEL.pdb MBP1_SCHPO APSES domain model coordinates] | * [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/MBP1_SCHPO_APSES_MODEL.pdb MBP1_SCHPO APSES domain model coordinates] | ||
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| + | [[Category:Bioinformatics]] | ||
| + | </div> | ||
Revision as of 18:14, 4 November 2012
Homology Modeling
Fallback Data
Here are results from a homology modeling exercise using SwissModel, as a fallback for technical problems with the assignment i.e network problems or other issues with the program or input data.
Contents
Target sequence
This is just one of the reference species' sequences - I chose Mbp1_SCHPO because it is the most distantly related to saccharomyces cerevisiae.
>MBP1_SCHPO NP_593032 23..96 IKGVSVMRRRRDSWLNATQILKVADFDKPQRTRVLERQVQIGAHEKVQGGYGKYQGTWVPFQRGVDLATK YKV
FASTA formatted target-template alignment
This uses the 1BM8 PDB file as template, the sequence was extracted from coordinates using the WhatIf server.
>1BM8_A QIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRI LEKEVLKETHEKVQGGFGKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDF >Mbp1_SCHPO 2-100 NP_593032 AVHVAVYSGVEVYECFIKGVSVMRRRRDSWLNATQILKVADFDKPQRTRV LERQVQIGAHEKVQGGYGKYQGTWVPFQRGVDLATKYKVDGIMSPILSL
[TBC once the SwissModel server is back...]
SwissModel response
Explanation of the output is found in the SwissModel Help page.
Graphical comparison of template and target sequence to emphasize which regions have been modelled.
Model QMEAN score vs. expected QMean scores of protein structures, as a function of domain size.
Cartoon view of the model, colored by QMEAN scores
The target-template alignment:
TARGET 1 IK -GVSVMRRRR DSWLNATQIL KVADFDKPQR
1mb1A 3 nqiysarysg vdvyef--ih stgsimkrkk ddwvnathil kaanfakakr
TARGET ssshhhh hh hhhh
1mb1A sssssss ssssss ss sssssss ssshhhh hh hhhh
TARGET 32 TRVLERQVQI GAHEKVQGGY GKYQGTWVPF QRGVDLATK ----------
1mb1A 51 trilekevlk ethekvqggf gkyqgtwvpl niakqlaekf svydqlkplf
TARGET hhhhhhhhh sss ssss h hhhhhhhhh
1mb1A hhhhh sss ssss h hhhhhhhhh hh hh
Local quality estimation: ANOLEA and QMEAN scores as graphical output
Model coordinates
