Difference between revisions of "Task4 Hemochromatosis Protocol"
Bernhoferm (talk | contribs) (→Evaluation) |
Bernhoferm (talk | contribs) (→Evaluation) |
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cd .. |
cd .. |
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done |
done |
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+ | </source> |
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+ | |||
+ | |||
+ | These scores were then extracted with a perl script: |
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+ | |||
+ | <source lang="perl"> |
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+ | #!/usr/local/bin/perl |
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+ | use strict; |
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+ | use warnings; |
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+ | use diagnostics; |
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+ | use sigtrap; |
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+ | use autodie; |
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+ | |||
+ | my $targetdir = "./"; |
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+ | my $outFileNative = "native.txt"; |
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+ | my $outFileComplex = "complex.txt"; |
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+ | |||
+ | opendir (DIR, $targetdir) or die ("Could not open directory!"); |
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+ | |||
+ | my @content= readdir(DIR); |
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+ | |||
+ | closedir(DIR); |
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+ | |||
+ | open (NATIVE, ">", $outFileNative) or die ("Could not open file!"); |
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+ | open (COMPLEX, ">", $outFileComplex) or die ("Could not open file!"); |
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+ | |||
+ | #print headers |
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+ | print NATIVE "<figtable id=\"scores_native\">\n"; |
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+ | print NATIVE "{| class=\"wikitable\" style=\"width: 65%; margin: 1em 1em 1em 0; border-collapse: collapse; border-style: solid; border-width:0px; border-color: #000\"\n"; |
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+ | print NATIVE "|-\n"; |
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+ | print NATIVE "! style=\"text-align:left; border-style: solid; border-width: 0 0 2px 0\" |Model\n"; |
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+ | print NATIVE "! style=\"text-align:left; border-style: solid; border-width: 0 0 2px 0\" |Common residues\n"; |
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+ | print NATIVE "! style=\"text-align:left; border-style: solid; border-width: 0 0 2px 0\" |TM-Score\n"; |
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+ | print NATIVE "! style=\"text-align:left; border-style: solid; border-width: 0 0 2px 0\" |GDT-TS\n"; |
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+ | print NATIVE "! style=\"text-align:left; border-style: solid; border-width: 0 0 2px 0\" |GDT-HA\n"; |
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+ | print NATIVE "! style=\"text-align:left; border-style: solid; border-width: 0 0 2px 0\" |TM-Align\n"; |
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+ | print NATIVE "! style=\"text-align:left; border-style: solid; border-width: 0 0 2px 0\" |Weighted RMSD\n"; |
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+ | print NATIVE "|-\n"; |
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+ | |||
+ | print COMPLEX "<figtable id=\"scores_complex\">\n"; |
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+ | print COMPLEX "{| class=\"wikitable\" style=\"width: 65%; margin: 1em 1em 1em 0; border-collapse: collapse; border-style: solid; border-width:0px; border-color: #000\"\n"; |
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+ | print COMPLEX "|-\n"; |
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+ | print COMPLEX "! style=\"text-align:left; border-style: solid; border-width: 0 0 2px 0\" |Model\n"; |
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+ | print COMPLEX "! style=\"text-align:left; border-style: solid; border-width: 0 0 2px 0\" |Common residues\n"; |
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+ | print COMPLEX "! style=\"text-align:left; border-style: solid; border-width: 0 0 2px 0\" |TM-Score\n"; |
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+ | print COMPLEX "! style=\"text-align:left; border-style: solid; border-width: 0 0 2px 0\" |GDT-TS\n"; |
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+ | print COMPLEX "! style=\"text-align:left; border-style: solid; border-width: 0 0 2px 0\" |GDT-HA\n"; |
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+ | print COMPLEX "! style=\"text-align:left; border-style: solid; border-width: 0 0 2px 0\" |TM-Align\n"; |
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+ | print COMPLEX "! style=\"text-align:left; border-style: solid; border-width: 0 0 2px 0\" |Weighted RMSD\n"; |
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+ | print COMPLEX "|-\n"; |
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+ | |||
+ | |||
+ | foreach my $dir (@content) |
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+ | { |
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+ | if (not $dir=~m/\./gi) |
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+ | { |
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+ | print "Extracting scores for $dir...\n"; |
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+ | my @nativeTM = extractTM("$dir/$dir\_native.tmscore"); |
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+ | my @complexTM = extractTM("$dir/$dir\_complex.tmscore"); |
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+ | my @nativeTMA = extractTMA("$dir/$dir\_native.tmalign"); |
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+ | my @complexTMA = extractTMA("$dir/$dir\_complex.tmalign"); |
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+ | my @nativeRMSD = extractRMSD("$dir/$dir\_native.rmsd"); |
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+ | my @complexRMSD = extractRMSD("$dir/$dir\_complex.rmsd"); |
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+ | |||
+ | print NATIVE "| style=\"border-style: solid; border-width: 0 0 0 0\" |$dir\n"; |
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+ | print NATIVE "| style=\"border-style: solid; border-width: 0 0 0 0\" |$nativeTM[0]\n"; |
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+ | print NATIVE "| style=\"border-style: solid; border-width: 0 0 0 0\" |$nativeTM[1]\n"; |
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+ | print NATIVE "| style=\"border-style: solid; border-width: 0 0 0 0\" |$nativeTM[2]\n"; |
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+ | print NATIVE "| style=\"border-style: solid; border-width: 0 0 0 0\" |$nativeTM[3]\n"; |
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+ | print NATIVE "| style=\"border-style: solid; border-width: 0 0 0 0\" |$nativeTMA[0]\n"; |
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+ | print NATIVE "| style=\"border-style: solid; border-width: 0 0 0 0\" |$nativeRMSD[1] (over $nativeRMSD[0] atoms)\n"; |
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+ | print NATIVE "|-\n"; |
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+ | |||
+ | print COMPLEX "| style=\"border-style: solid; border-width: 0 0 0 0\" |$dir\n"; |
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+ | print COMPLEX "| style=\"border-style: solid; border-width: 0 0 0 0\" |$complexTM[0]\n"; |
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+ | print COMPLEX "| style=\"border-style: solid; border-width: 0 0 0 0\" |$complexTM[1]\n"; |
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+ | print COMPLEX "| style=\"border-style: solid; border-width: 0 0 0 0\" |$complexTM[2]\n"; |
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+ | print COMPLEX "| style=\"border-style: solid; border-width: 0 0 0 0\" |$complexTM[3]\n"; |
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+ | print COMPLEX "| style=\"border-style: solid; border-width: 0 0 0 0\" |$complexTMA[0]\n"; |
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+ | print COMPLEX "| style=\"border-style: solid; border-width: 0 0 0 0\" |$complexRMSD[1] (over $complexRMSD[0] atoms)\n"; |
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+ | print COMPLEX "|-\n"; |
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+ | } |
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+ | } |
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+ | |||
+ | print NATIVE "|+ style=\"caption-side: bottom; text-align: left\" | <font size=1>'''TODO''': NATIVE.\n"; |
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+ | print NATIVE "|}\n"; |
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+ | print NATIVE "</figtable>\n"; |
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+ | |||
+ | print COMPLEX "|+ style=\"caption-side: bottom; text-align: left\" | <font size=1>'''TODO''': COMPLEX.\n"; |
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+ | print COMPLEX "|}\n"; |
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+ | print COMPLEX "</figtable>\n"; |
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+ | |||
+ | close COMPLEX; |
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+ | close NATIVE; |
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+ | |||
+ | |||
+ | sub extractTM |
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+ | { |
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+ | my $filename = $_[0]; |
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+ | |||
+ | open (FILE, "<", $filename) or die "Could not open file!"; |
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+ | |||
+ | my $commonResidues = ""; |
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+ | my $tmScore = ""; |
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+ | my $gdttsScore = ""; |
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+ | my $gdthaScore = ""; |
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+ | |||
+ | while (<FILE>) |
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+ | { |
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+ | my $line = $_; |
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+ | |||
+ | if ($line=~m/^Number\sof\sresidues\sin\scommon\s*?=\s*?(\S+?)\s+?/gi) |
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+ | { |
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+ | $commonResidues = $1; |
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+ | } |
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+ | elsif ($line=~m/^TM-score\s*?=\s*?(\S+?)\s+?/gi) |
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+ | { |
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+ | $tmScore = $1; |
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+ | } |
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+ | elsif ($line=~m/^GDT-TS-score\s*?=\s*?(\S+?)\s+?/gi) |
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+ | { |
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+ | $gdttsScore = $1; |
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+ | } |
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+ | elsif ($line=~m/^GDT-HA-score\s*?=\s*?(\S+?)\s+?/gi) |
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+ | { |
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+ | $gdthaScore = $1; |
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+ | } |
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+ | } |
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+ | |||
+ | print $commonResidues."\t"; |
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+ | print $tmScore."\t"; |
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+ | print $gdttsScore."\t"; |
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+ | print $gdthaScore."\n"; |
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+ | |||
+ | close FILE; |
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+ | |||
+ | return ($commonResidues, $tmScore, $gdttsScore, $gdthaScore); |
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+ | } |
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+ | |||
+ | |||
+ | sub extractTMA |
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+ | { |
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+ | my $filename = $_[0]; |
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+ | |||
+ | open (FILE, "<", $filename) or die "Could not open file!"; |
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+ | |||
+ | my $tmScore = ""; |
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+ | |||
+ | while (<FILE>) |
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+ | { |
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+ | my $line = $_; |
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+ | |||
+ | if ($line=~m/TM-score\s*?=\s*?(\S+?)\s*?,/gi) |
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+ | { |
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+ | $tmScore = $1; |
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+ | } |
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+ | } |
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+ | |||
+ | print $tmScore."\n"; |
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+ | |||
+ | close FILE; |
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+ | |||
+ | return ($tmScore); |
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+ | } |
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+ | |||
+ | |||
+ | sub extractRMSD |
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+ | { |
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+ | my $filename = $_[0]; |
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+ | |||
+ | open (FILE, "<", $filename) or die "Could not open file!"; |
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+ | |||
+ | my $commonResidues = ""; |
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+ | my $rmsdScore = ""; |
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+ | |||
+ | while (<FILE>) |
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+ | { |
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+ | my $line = $_; |
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+ | |||
+ | if ($line=~m/^Weighted\sRMSd\s*?=\s*?(\S+?)\s*?\(over\s*?(\S+?)\s+?/gi) |
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+ | { |
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+ | $rmsdScore = $1; |
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+ | $commonResidues = $2; |
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+ | } |
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+ | } |
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+ | |||
+ | print $commonResidues."\t"; |
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+ | print $rmsdScore."\n"; |
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+ | |||
+ | close FILE; |
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+ | |||
+ | return ($commonResidues, $rmsdScore); |
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+ | } |
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</source> |
</source> |
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Revision as of 00:12, 4 June 2012
Contents
Template search
Query sequence used: Q30201
HHPred
We used HHPred (Webserver) to search for homologs. Standard parameters were used (DB: pdb70_15May12).
Weblink to results (as long as they are online): results
COMA
Another search was performed using COMA (Webserver). Again standard parameters were kept (DB: pdb40_2012-03-22).
Weblink to results (as long as they are online): results
Model creation
Modeller
SwissModel
We used the Webserver to produce our models.
I-Tasser
For I-Tasser we also used the Webserver, but with Option I to specify our template (without alignment).
Evaluation
For the native structure we used 1a6z and 1de4 for the complex structure.
A bash script was used to run TM-Score, TM-Align, and SAP for our models:
<source lang="bash">
- !/bin/bash
TMSCORE="/mnt/project/pracstrucfunc12/bin/TMscore" TMALIGN="/mnt/project/pracstrucfunc12/bin/TMalign" RMSD="/mnt/project/pracstrucfunc12/bin/sap"
for model in `ls | grep .pdb` do MODELNAME=${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>
These scores were then extracted with a perl script:
<source lang="perl">
- !/usr/local/bin/perl
use strict; use warnings; use diagnostics; use sigtrap; use autodie;
my $targetdir = "./"; my $outFileNative = "native.txt"; my $outFileComplex = "complex.txt";
opendir (DIR, $targetdir) or die ("Could not open directory!");
my @content= readdir(DIR);
closedir(DIR);
open (NATIVE, ">", $outFileNative) or die ("Could not open file!"); open (COMPLEX, ">", $outFileComplex) or die ("Could not open file!");
- print headers
print NATIVE "<figtable id=\"scores_native\">\n"; print NATIVE "{| class=\"wikitable\" style=\"width: 65%; margin: 1em 1em 1em 0; border-collapse: collapse; border-style: solid; border-width:0px; border-color: #000\"\n"; print NATIVE "|-\n"; print NATIVE "! style=\"text-align:left; border-style: solid; border-width: 0 0 2px 0\" |Model\n"; print NATIVE "! style=\"text-align:left; border-style: solid; border-width: 0 0 2px 0\" |Common residues\n"; print NATIVE "! style=\"text-align:left; border-style: solid; border-width: 0 0 2px 0\" |TM-Score\n"; print NATIVE "! style=\"text-align:left; border-style: solid; border-width: 0 0 2px 0\" |GDT-TS\n"; print NATIVE "! style=\"text-align:left; border-style: solid; border-width: 0 0 2px 0\" |GDT-HA\n"; print NATIVE "! style=\"text-align:left; border-style: solid; border-width: 0 0 2px 0\" |TM-Align\n"; print NATIVE "! style=\"text-align:left; border-style: solid; border-width: 0 0 2px 0\" |Weighted RMSD\n"; print NATIVE "|-\n";
print COMPLEX "<figtable id=\"scores_complex\">\n"; print COMPLEX "{| class=\"wikitable\" style=\"width: 65%; margin: 1em 1em 1em 0; border-collapse: collapse; border-style: solid; border-width:0px; border-color: #000\"\n"; print COMPLEX "|-\n"; print COMPLEX "! style=\"text-align:left; border-style: solid; border-width: 0 0 2px 0\" |Model\n"; print COMPLEX "! style=\"text-align:left; border-style: solid; border-width: 0 0 2px 0\" |Common residues\n"; print COMPLEX "! style=\"text-align:left; border-style: solid; border-width: 0 0 2px 0\" |TM-Score\n"; print COMPLEX "! style=\"text-align:left; border-style: solid; border-width: 0 0 2px 0\" |GDT-TS\n"; print COMPLEX "! style=\"text-align:left; border-style: solid; border-width: 0 0 2px 0\" |GDT-HA\n"; print COMPLEX "! style=\"text-align:left; border-style: solid; border-width: 0 0 2px 0\" |TM-Align\n"; print COMPLEX "! style=\"text-align:left; border-style: solid; border-width: 0 0 2px 0\" |Weighted RMSD\n"; print COMPLEX "|-\n";
foreach my $dir (@content)
{
if (not $dir=~m/\./gi)
{
print "Extracting scores for $dir...\n";
my @nativeTM = extractTM("$dir/$dir\_native.tmscore");
my @complexTM = extractTM("$dir/$dir\_complex.tmscore");
my @nativeTMA = extractTMA("$dir/$dir\_native.tmalign");
my @complexTMA = extractTMA("$dir/$dir\_complex.tmalign");
my @nativeRMSD = extractRMSD("$dir/$dir\_native.rmsd");
my @complexRMSD = extractRMSD("$dir/$dir\_complex.rmsd");
print NATIVE "| style=\"border-style: solid; border-width: 0 0 0 0\" |$dir\n"; print NATIVE "| style=\"border-style: solid; border-width: 0 0 0 0\" |$nativeTM[0]\n"; print NATIVE "| style=\"border-style: solid; border-width: 0 0 0 0\" |$nativeTM[1]\n"; print NATIVE "| style=\"border-style: solid; border-width: 0 0 0 0\" |$nativeTM[2]\n"; print NATIVE "| style=\"border-style: solid; border-width: 0 0 0 0\" |$nativeTM[3]\n"; print NATIVE "| style=\"border-style: solid; border-width: 0 0 0 0\" |$nativeTMA[0]\n"; print NATIVE "| style=\"border-style: solid; border-width: 0 0 0 0\" |$nativeRMSD[1] (over $nativeRMSD[0] atoms)\n"; print NATIVE "|-\n";
print COMPLEX "| style=\"border-style: solid; border-width: 0 0 0 0\" |$dir\n"; print COMPLEX "| style=\"border-style: solid; border-width: 0 0 0 0\" |$complexTM[0]\n"; print COMPLEX "| style=\"border-style: solid; border-width: 0 0 0 0\" |$complexTM[1]\n"; print COMPLEX "| style=\"border-style: solid; border-width: 0 0 0 0\" |$complexTM[2]\n"; print COMPLEX "| style=\"border-style: solid; border-width: 0 0 0 0\" |$complexTM[3]\n"; print COMPLEX "| style=\"border-style: solid; border-width: 0 0 0 0\" |$complexTMA[0]\n"; print COMPLEX "| style=\"border-style: solid; border-width: 0 0 0 0\" |$complexRMSD[1] (over $complexRMSD[0] atoms)\n"; print COMPLEX "|-\n"; } }
print NATIVE "|+ style=\"caption-side: bottom; text-align: left\" | TODO: NATIVE.\n"; print NATIVE "|}\n"; print NATIVE "</figtable>\n";
print COMPLEX "|+ style=\"caption-side: bottom; text-align: left\" | TODO: COMPLEX.\n"; print COMPLEX "|}\n"; print COMPLEX "</figtable>\n";
close COMPLEX; close NATIVE;
sub extractTM
{
my $filename = $_[0];
open (FILE, "<", $filename) or die "Could not open file!";
my $commonResidues = ""; my $tmScore = ""; my $gdttsScore = ""; my $gdthaScore = "";
while (<FILE>) { my $line = $_;
if ($line=~m/^Number\sof\sresidues\sin\scommon\s*?=\s*?(\S+?)\s+?/gi) { $commonResidues = $1; } elsif ($line=~m/^TM-score\s*?=\s*?(\S+?)\s+?/gi) { $tmScore = $1; } elsif ($line=~m/^GDT-TS-score\s*?=\s*?(\S+?)\s+?/gi) { $gdttsScore = $1; } elsif ($line=~m/^GDT-HA-score\s*?=\s*?(\S+?)\s+?/gi) { $gdthaScore = $1; } }
print $commonResidues."\t"; print $tmScore."\t"; print $gdttsScore."\t"; print $gdthaScore."\n";
close FILE;
return ($commonResidues, $tmScore, $gdttsScore, $gdthaScore); }
sub extractTMA
{
my $filename = $_[0];
open (FILE, "<", $filename) or die "Could not open file!";
my $tmScore = "";
while (<FILE>) { my $line = $_;
if ($line=~m/TM-score\s*?=\s*?(\S+?)\s*?,/gi) { $tmScore = $1; } }
print $tmScore."\n";
close FILE;
return ($tmScore); }
sub extractRMSD
{
my $filename = $_[0];
open (FILE, "<", $filename) or die "Could not open file!";
my $commonResidues = ""; my $rmsdScore = "";
while (<FILE>) { my $line = $_;
if ($line=~m/^Weighted\sRMSd\s*?=\s*?(\S+?)\s*?\(over\s*?(\S+?)\s+?/gi) { $rmsdScore = $1; $commonResidues = $2; } }
print $commonResidues."\t"; print $rmsdScore."\n";
close FILE;
return ($commonResidues, $rmsdScore); } </source>
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