Difference between revisions of "Task4 Hemochromatosis Protocol"
Bernhoferm (talk | contribs) (→I-Tasser) |
Bernhoferm (talk | contribs) (→Evaluation) |
||
| Line 46: | Line 46: | ||
== Evaluation == |
== Evaluation == |
||
| + | |||
| + | We used a bash script to run TM-Score, TM-Align, and SAP for our models: |
||
| + | |||
| + | <source lang="bash"> |
||
| + | #!/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 $MODELNAME"_complex_super.pdb" |
||
| + | cd .. |
||
| + | done |
||
| + | </source> |
||
== Other == |
== Other == |
||
Revision as of 12:03, 1 June 2012
Contents
Template search
Query sequence used: Q30201
HHPred
We used HHPred (Webserver) to search for homologs. Standard parameters were used (DB: pdb70_15May12).
Weblink to results (as long as they are online): results
COMA
Another search was performed using COMA (Webserver). Again standard parameters were kept (DB: pdb40_2012-03-22).
Weblink to results (as long as they are online): results
Model creation
Modeller
SwissModel
We used the Webserver to produce our models.
I-Tasser
For I-Tasser we also used the Webserver, but with Option I to specify our template (without alignment).
Evaluation
We used a bash script to run TM-Score, TM-Align, and SAP for our models:
<source lang="bash">
- !/bin/bash
TMSCORE="/mnt/project/pracstrucfunc12/bin/TMscore" TMALIGN="/mnt/project/pracstrucfunc12/bin/TMalign" RMSD="/mnt/project/pracstrucfunc12/bin/sap"
for model in `ls | grep .pdb` do MODELNAME=${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>
