| "; print " Summary of Input |
| "; print "Scaffold Structure"; print " | "; } else { print "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| "; print "Scaffold Structure"; print " | "; } if(file_exists($receptorFile)) { print ""; print "Receptor Structure"; print " | "; print ""; print " Complex Structure "; print " | "; print "|
| \n"; if(file_exists($receptorFile)) { print " | \n"; if(is_file($complexPDB)) { print" | \n"; } else { print " | Generating complex via docking. . . | "; } } print "
";
$filename="./summary.txt";
if(file_exists($filename) == True) {
} else {
print "
";
print "Your submission has been received and the job is running. . .";
}
################ print output ------------------>
if(is_file($filename) == True) {
#print "$align";
print "
";
print "
| "; print " Top 10 Structural Homologs Used for Profile Construction |
| Rank | PDB Hit | TM-score | Iden. | "; print " | ";
$ss=file("./SS.txt");
chop($splitSS=explode(":",$ss[3]));
$secStr = str_split($splitSS[1]);
$seqLength =0;
foreach ($secStr as $value) {
if($value!=' ') {
if($value == "C") {
$seqLength++;
} elseif($value == "H") {
$seqLength++;
} elseif($value == "E") {
$seqLength++;
}
}
}
$i =1;
while($i<=$seqLength) {
if(is_int($i/20)) {
print "$i";
$i=$i+mb_strlen($i);
} else {
print " ";
$i++;
}
}
print " "; for($k=1;$k<=$seqLength;$k++) { if(is_int($k/20)) { print "|"; } else { print " "; } } print " | |||
|---|---|---|---|---|---|---|---|---|
| Sec.Str Seq | ";
foreach ($secStr as $value) {
if ($value!=' ') {
if($value == "C") {
print "C";
$seqLength++;
} elseif($value == "H") {
print "H";
$seqLength++;
} elseif($value == "E") {
print "E";
$seqLength++;
}
}
}
print " "; $scaffold=file("./SI.txt"); chop($splitScaffold=explode(":",$scaffold[2])); $expScaffold= str_split($splitScaffold[1]); foreach($expScaffold as $scaffAA) { if($scaffAA!=' ') { print $scaffAA; } } print " | |||||||
| $rank | "; print "$splitMSA[0] | "; $TMscore=round($splitMSA[1],2); print "$TMscore | "; $seq=str_split($splitMSA[2]); $seqIDindex=$rank-1; $ID = round($tempSeqID[$seqIDindex],2); print "$ID | "; print ""; # print "$scaffAA[1]"; print " | "; foreach ($seq as $AA) { if($AA!=' ') { if ($AA == $scaffAA[$scaffIndex]) { if ($AA == "D" || $AA == "E") { print "$AA"; } elseif($AA == "G" || $AA == "H") { print "$AA"; } elseif($AA == "L" || $AA=="I") { print "$AA"; } elseif($AA == "F" || $AA=="Y") { print "$AA"; } elseif($AA =="C" || $AA=="M") { print "$AA"; } elseif ($AA=="A") { print "$AA"; } elseif ($AA == "P") { print "$AA"; } elseif ($AA=="N" || $AA =="Q") { print "$AA"; } elseif ($AA =="W") { print "$AA"; } elseif($AA=="V") { print "$AA"; } elseif($AA=="S" || $AA == "T") { print "$AA"; } elseif($AA=="R" || $AA=="K") { print "$AA"; } } else { print "$AA"; } $scaffIndex++; } } print " | |||
";
print "
|
| "; print " Clustering Results |
| Sequences generated during the Monte Carlo simulation are clustered. The top clusters are listed in the table below. Information in the table includes the relative cluster sizes as well as the number of the top sequences that originate from each cluster. Users are able to download every sequence in each cluster; the files include the sequences as well as the free-energy of each sequence predicted by EvoDesign. | "; print "
| Cluster Number | Relative Cluster Size | # Sequences Selected from Cluster | Download Each Sequence in Cluster |
|---|---|---|---|
| $splitLine[0] | "; print "$splitLine[1]% | "; print "$splitLine[2] | "; print "Clus $splitLine[0] Sequences | "; } print "
| "; print " Summary of Output |
| Design Number | Sequence Identity (%) |
Normalized Relative Error [?] | |||
| Secondary Structure | Solvent Accessibility | Torsion Angle φ | Torsion Angle ψ | EvoDesign Score |
$count=0;
$fp=fopen("./summary.txt","r");
while(!feof($fp)) {
$aline=fgets($fp,4096);
chop($aline);
if(feof($fp)) { break; }
$lineSummary[$count]=$aline;
$count++;
}
fclose($fp);
for($i=1;$i<$count;$i++) {
$summary=explode(',',$lineSummary[$i]);
if($summary[1]>0.01) {
$score=10/$summary[1];
} else {
$score=1001;
}
# | ";
#printf("%6.2f",$score);
$seqIDDes[$i]=$summary[2];
print "
| ";
print "Data.zip |
SI |
SS |
SA |
φ |
ψ |
|
| (a) | Sequence Identity: The percent sequence identity between the designed sequence and the scaffold sequence. |
| (b) | Normalized Relative Error (NRE): NRE=(EDSāETS)/ETS, where EDS is the error of the neural-network predictions relative to the scaffold structure on the design sequence and ETS is the error of the predictions based on the sequence of the target scaffold. The secondary structure, solvent accessibility and torsion angles for the scaffold structure are assigned by DSSP. |
| (c) | Secondary Structure (SS): SS is predicted by PSSPred for the scaffold and design sequences. The Q3 errors of the design sequence (EDS) and scaffold sequence (ETS) with respect to the scaffold structure are used to calculate the NRE for SS. |
| (d) | Solvent Accessibility (SA): SA for scaffold and design sequences are predicted by neural-network method. The correlation on SA between design sequence and scaffold structure (EDS) and between scaffold sequence and scaffold structure (ETS) is used to calculate NRE on SA. |
| (e) | Torsion Angle (TA): TA is predicted by ANGLOR for scaffold and design sequences. The mean absolute difference of the design sequence (EDS) and scaffold sequence (ETS) from the scaffold structure is used to calculate NRE for TA. |
SeqIdentity: $summary[2]%"; # print "$message"; # } # } print "
"; # $fp=fopen($filename,"r"); # while(!feof($fp)) { # $aline=fgets($fp,4096); # chop($aline); # $message.=" $aline"; # } # fclose($fp); # $message.="
| "; print " Final Designed Sequences |
Energy: EvoDesign calculated free energy of binding and folding"; print "$message"; print "
"; $message.="Iden.: % of sequence identity between design sequence and scaffold sequence.
"; $fp=fopen("../des1.txt","r"); while(!feof($fp)) { $aline=fgets($fp,4096); chop($aline); $pos=strpos($aline,"bind"); if($pos == false) { } else { $message.="Lig_bind: Residues are within 8.0 Å sphere radius of the hetero atoms.
"; } break; } fclose($fp); $message.="DSSP_SS: Secondary structure as assigned by DSSP program on the scaffold structure.
"; $message.="Scaffold: Scaffold sequence.
"; $message.=" The identical residues are marked by '|'.
"; $message.="Design: Design sequence.
| Click to view | Cluster 1 Designs | Energy |
|---|
| "; print " Cluster $cluster Center |
| Design Number | Energy | Iden. (%) | ||||||
|---|---|---|---|---|---|---|---|---|
| $j | "; print "$energy[$energyIndex] | "; $energyIndex++; print "$seqIDDes[$j] | "; print " DSSP_SS Scaffold Design$j | ";
$ssIndex=3+$j;
chop($splitSS=explode(":",$ss[$ssIndex]));
$secStr = str_split($splitSS[1]);
foreach ($secStr as $value) {
if($value == "C") {
print "C";
} elseif($value == "H") {
print "H";
} elseif($value=="E") {
print "E";
}
}
fclose($fp);
print " "; $scaffold=file("./SI.txt"); chop($splitScaffold=explode(":",$scaffold[2])); print "$splitScaffold[1]"; print " "; $dashFile=file("./des$j.txt"); chop($dashes=$dashFile[2]); $splitDash=str_split($dashes); $count =1; foreach($splitDash as $value) { if ($count >=17) { if ($value==' ') { print " "; } else { print "$value"; } } $count++; } print " "; #$dashFile=file("../des$j.txt"); #chop($dashes=$dashFile[2]); #print "$dashes"; #print " "; chop($desSeq=explode(":",$dashFile[3])); print "$desSeq[1]"; print " | \n";
print "
| "; print " Cluster $cluster Lowest Energy Sequences |
| Design Number | Energy | Iden. (%) | |||||||
|---|---|---|---|---|---|---|---|---|---|
| $j | "; print "$energy[$energyIndex] | "; $energyIndex++; print "$seqIDDes[$j] | "; # print ""; # print ""; # print " | "; $countColor=2; } else { if($countColor % 2==0) { print "||||||
| $j | "; print "$energy[$index] | "; print "$seqIDDes[$j] | "; # print ""; # print ""; # print " | "; $countColor++; } else { print "||||||
| $j | "; print "$energy[$index] | "; print "$seqIDDes[$j] | "; # print ""; # print ""; # print " | "; $countColor++; } } #print"div id=\"seq$j\">;"; print " DSSP_SS Scaffold Design$j | ";
foreach ($secStr as $value) {
if($value == "C") {
print "C";
} elseif($value == "H") {
print "H";
} elseif($value=="E") {
print "E";
}
}
print " "; $hideSeq[$cluster][$j]=$j; print "$splitScaffold[1]"; print " "; $dashFile=file("./des$j.txt"); chop($dashes=$dashFile[2]); $splitDash=str_split($dashes); $count =1; foreach($splitDash as $value) { if ($count >=17) { if ($value==' ') { print " "; } else { print "$value"; } } $count++; } print " "; chop($desSeq=explode(":",$dashFile[3])); print "$desSeq[1]"; print " | \n";
print "||||
"; print "
| "; #print " Predicted Secondary Structure of Designed Sequences |
| "; #print " Predicted Solvent Accessibility of Designed Sequences |
| "; print " I-TASSER Modeling of Designed Sequences |
| Models of Top 10 Designed Sequences "; print "
|
";
}
print "
\n";
print "