Task4 Hemochromatosis Protocol

Template search

Query sequence used: Q30201

HHPred

We used HHPred (Webserver) to search for homologs. Standard parameters were used (DB: pdb70_15May12).

Weblink to results (as long as they are online): results

COMA

Another search was performed using COMA (Webserver). Again standard parameters were kept (DB: pdb40_2012-03-22).

Weblink to results (as long as they are online): results

Model creation

SwissModel

We used the Webserver to produce our models.

I-Tasser

For I-Tasser we also used the Webserver, but with Option I to specify our template (without alignment).

Evaluation

For the native structure we used 1a6z and 1de4 for the complex structure. We used a bash script to run TM-Score, TM-Align, and SAP for our models:

<source lang="bash">

1. !/bin/bash

TMSCORE="/mnt/project/pracstrucfunc12/bin/TMscore" TMALIGN="/mnt/project/pracstrucfunc12/bin/TMalign" RMSD="/mnt/project/pracstrucfunc12/bin/sap"

for model in `ls | grep .pdb` do MODELNAME=${model%.[^.]*} echo "Processing model: "$MODELNAME mkdir -p $MODELNAME cd $MODELNAME $TMSCORE ../$model ../1a6z.ent -o $MODELNAME"_native_tm.sup" > $MODELNAME"_native.tmscore" $TMSCORE ../$model ../1de4.ent -o $MODELNAME"_complex_tm.sup" > $MODELNAME"_complex.tmscore" $TMALIGN ../$model ../1a6z.ent -o $MODELNAME"_native_align.sup" > $MODELNAME"_native.tmalign" $TMALIGN ../$model ../1de4.ent -o $MODELNAME"_complex_align.sup" > $MODELNAME"_complex.tmalign" $RMSD ../$model ../1a6z.ent > $MODELNAME"_native.rmsd" mv super.pdb $MODELNAME"_native_super.pdb" $RMSD ../$model ../1de4.ent > $MODELNAME"_complex.rmsd" mv super.pdb $MODELNAME"_complex_super.pdb" cd .. done </source>