Difference between revisions of "Homology-based structure prediction (PKU)"

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(PDBe)
(PDBe)
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These datasets were derived from serveral sources. They all consist of PDB-entries, but we ensured to no include the already known structure of our protein, so we have a better insight in the topic of homology modeling with a completely unknown sequence.
 
These datasets were derived from serveral sources. They all consist of PDB-entries, but we ensured to no include the already known structure of our protein, so we have a better insight in the topic of homology modeling with a completely unknown sequence.
 
====PDBe====
 
====PDBe====
For this set of datasets we used the webservice of sequence similarity search provieded by the pdb called PDBeXplore, which can be accessed [http://www.ebi.ac.uk/pdbe-srv/PDBeXplore/sequence/ here]
+
For this set of datasets we used the webservice of sequence similarity search provieded by the pdb called PDBeXplore, which can be accessed [http://www.ebi.ac.uk/pdbe-srv/PDBeXplore/sequence/ here]. In the used dataset (see <xr id="tab:datasetpdbe" /> we restricted the received data from pdb, such as we didnt use the structure of both the monomer and the dimer etc. We also did not use the structure with different ligands in order to keep the variability high.
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<div style="float:left; border:thin solid lightgrey; margin-right: 20px;">
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<figtable id="tab:datasetpdbe">
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<caption>Dataset PDBe</caption>
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{| style="border-collapse: separate; border-spacing: 0; border-width: 1px; border-style: solid; padding-left:5px; padding-right:5px; border-color: #000; padding: 0"
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! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| pdb ID
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! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| E-value
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! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0; text-align: right"| Identity in %
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|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 1px 0 1px 0;" colspan = "3"| > 80% sequence identity
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|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0; font-style:italic;"| [http://www.pdb.org/pdb/search/structidSearch.do?structureId=2phm 2phm]
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 4.1e-148
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0; text-align: right"| 95.5
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|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 1px 0 1px 0;" colspan = "3"| 40% - 80% sequence identity
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|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0; font-style:italic;"| [http://www.pdb.org/pdb/search/structidSearch.do?structureId=2xsn 2xsn]
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 6e-100
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0; text-align: right"| 61.1
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|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0; font-style:italic;"| [http://www.pdb.org/pdb/search/structidSearch.do?structureId=1toh 1toh]
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 1e-99
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0; text-align: right"| 60.8
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|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0; font-style:italic;"| [http://www.pdb.org/pdb/search/structidSearch.do?structureId=3e2t 3e2t]
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 8.5e-99
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0; text-align: right"| 64.4
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|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0; font-style:italic;"| [http://www.pdb.org/pdb/search/structidSearch.do?structureId=1mlw 1mlw]
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 1.1e-95
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0; text-align: right"| 66.1
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|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0; font-style:italic;"| [http://www.pdb.org/pdb/search/structidSearch.do?structureId=3hf8 3hf8]
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 1.5e-92
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0; text-align: right"| 66.4
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|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 1px 0 1px 0;" colspan = "3"| < 30% sequence identity
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|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0; font-style:italic;"| [http://www.pdb.org/pdb/search/structidSearch.do?structureId=3cc1 3cc1]
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 5.5e-74
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0; text-align: right"| 25
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|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0; font-style:italic;"| 1zy9
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 3.1e-48
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0; text-align: right"| 13
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|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0; font-style:italic;"| [http://www.pdb.org/pdb/search/structidSearch.do?structureId=3a24 3a24]
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 7.8e-40
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0; text-align: right"| 17
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|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0; font-style:italic;"| 2xn2
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 5.3e-37
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0; text-align: right"| 15
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|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0; font-style:italic;"| 2d73
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 5.7e-36
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0; text-align: right"| 14
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|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0; font-style:italic;"| 3mi6
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 1.4e-31
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0; text-align: right"| 15
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|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0; font-style:italic;"| 2yfo
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 9.1e-30
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0; text-align: right"| 13
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|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0; font-style:italic;"| 2f2h
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 2.7e-20
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0; text-align: right"| 17
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|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0; font-style:italic;"| 2g3m
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 2.2e-20
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0; text-align: right"| 16
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|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0; font-style:italic;"| 3nsx
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 6e-20
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0; text-align: right"| 13
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|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0; font-style:italic;"| 3lpp
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 2.2e-18
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0; text-align: right"| 15
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|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0; font-style:italic;"| 3l4y
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 1.9e-18
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0; text-align: right"| 15
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|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0; font-style:italic;"| 3top
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 3.6e-18
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0; text-align: right"| 12
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|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0; font-style:italic;"| 2xvl
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 3.2e-18
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0; text-align: right"| 16
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|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0; font-style:italic;"| 2x2h
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 4.9e-16
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0; text-align: right"| 13
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|-
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|}
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</figtable>
   
 
====HHPred====
 
====HHPred====

Revision as of 14:14, 29 May 2012

Short Task Description

After the sequence based predictions of function and secondary structure for our protein we will determine the 3D structure of the wild type protein and observe the influence one or several SNPs have on this structure. Of the variety of methods to be used for tertiary structure prediction, we choose homology modeling as a first approach to our goal. Read the complete task description here. The protocol of commands and scripts can be found in our journal

Model Construction

Here we will show the steps we took building the models we then use and evaluate. In order to start the sheer model-building we first have to construct some datasets, which will be the founding of our models.

Datasets

These datasets were derived from serveral sources. They all consist of PDB-entries, but we ensured to no include the already known structure of our protein, so we have a better insight in the topic of homology modeling with a completely unknown sequence.

PDBe

For this set of datasets we used the webservice of sequence similarity search provieded by the pdb called PDBeXplore, which can be accessed here. In the used dataset (see <xr id="tab:datasetpdbe" /> we restricted the received data from pdb, such as we didnt use the structure of both the monomer and the dimer etc. We also did not use the structure with different ligands in order to keep the variability high.

<figtable id="tab:datasetpdbe"> Dataset PDBe

pdb ID E-value Identity in %
> 80% sequence identity
2phm 4.1e-148 95.5
40% - 80% sequence identity
2xsn 6e-100 61.1
1toh 1e-99 60.8
3e2t 8.5e-99 64.4
1mlw 1.1e-95 66.1
3hf8 1.5e-92 66.4
< 30% sequence identity
3cc1 5.5e-74 25
1zy9 3.1e-48 13
3a24 7.8e-40 17
2xn2 5.3e-37 15
2d73 5.7e-36 14
3mi6 1.4e-31 15
2yfo 9.1e-30 13
2f2h 2.7e-20 17
2g3m 2.2e-20 16
3nsx 6e-20 13
3lpp 2.2e-18 15
3l4y 1.9e-18 15
3top 3.6e-18 12
2xvl 3.2e-18 16
2x2h 4.9e-16 13

</figtable>

HHPred

Coma

Modelevaluation