Homology-based structure prediction (PKU)
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
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.
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.
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|
|40% - 80% sequence identity|
|< 30% sequence identity|