Difference between revisions of "Team:Technion Israel/Software"

 
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<div class="col-md-12 col-sm-12">
 
<div class="col-md-12 col-sm-12">
−
<h1 class="text-center"><u>Software</u></h1><!--Headline-->
+
<!--Headline-->
−
<br>
+
 
<h2>Software tool</h2>
 
<h2>Software tool</h2>
−
<p class="text-justify">
 
−
We have worked hard the whole year to successfully redesigning ligand binding site of the Tar chemoreceptor
 
−
with Rosetta software, according to protocol presented in "Rosetta and the Design of Ligand Binding Sites" <b>(1)</b>.
 
−
The work we have achieved can be expanded into other receptors and ligands, and can be a use for other researchers.<br>
 
−
<br>
 
−
Our software tool offers the chance for fellow researcher to redesign ligand binding sites without inhibitions using
 
−
our automation script. One can do so in two ways: on his local computer cluster server or online with the form below.<br>
 
−
See the Rosetta page <b>(link to rosetta page)</b> for more explanations about the use of the software, and see the wet lab results of our designs.
 
−
</p><br>
 
  
 +
<div class="row">
 +
<div class="col-md-6 col-sm-12 vcenter"><!--6 text-->
 +
<p class="text-justify">
 +
We worked hard for many months to successfully redesign the ligand binding site of the <I>E. coli</I> Tar chemoreceptor. This feat was done using the Rosetta software suite by following the protocol published by <i>Moretti, R. et al.</i> <b>(1)</b>. The work we have achieved can be expanded into other receptors and ligands, and can be of use for other researchers.<br>
 +
 +
Our software tool offers fellow scientists the ability to design their own custom chemoreceptors by redesigning the Tar ligand binding site,
 +
and without needing to tackle the many challenges of Rosetta. One can do so in two ways:<br>
 +
1) Using a local installation of Rosetta (preferably on a computer cluster).<br>
 +
2) Online, with the form below.<br>
 
<br>
 
<br>
  
−
<h2>Using local server</h2>
+
</p>
 +
</div><!--
 +
--><div class="col-md-6 col-sm-12 vcenter"><!--6 img div-->
 +
<a class="pop ocenter">
 +
<img src="https://static.igem.org/mediawiki/2016/f/fb/T--Technion_Israel--software.png" class="img-responsive img-center" width="450" style="cursor: pointer;">
 +
</a>
 +
</div>
 +
</div>
 +
<div class="row">
 +
<div class="col-md-12 col-sm-12">
 +
<p class="text-justify">
 +
See the <a href="https://2016.igem.org/Team:Technion_Israel/Modifications/Rosetta" >Computational Design page</a> for more explanations about the use of the software, and see the wet lab results of our designs at the results tab.
 +
</p>
 +
</div>
 +
</div>
 +
 
 +
 
 +
 
 +
<h2>Using a local installation</h2>
 
<p class="text-justify">
 
<p class="text-justify">
−
We supply a zip file for Linux system with all necessary scripts to successfully run the redesigning automatically.  
+
We supply a zip file for a Linux system with all necessary scripts to successfully run the redesigning automatically. This script is used only as a framework for working with Rosetta. To successfully run it you are required to download and install the following software: Rosetta, BCL, OpenBabel, Python and a protein visualization program such as UCSF Chimera or PyMol.<br>
−
This scripts used only as a framework for working with Rosetta software, those you require to download and install:  
+
−
Rosetta software, BCL, OpenBable, Python and protein visualization program such as UCSF Chimera.<br>
+
 
<br>
 
<br>
−
<b>Install:</b> Download our <a href="https://static.igem.org/mediawiki/2016/0/00/Src.zip">software</a> to Linux operation  
+
<b>Installation:</b> Download our <a href="https://static.igem.org/mediawiki/2016/0/00/Src.zip">software</a> to Linux operation  
−
system and unzip it on the server where you install the rest of the programs, in the same folder you wish to save your  
+
system and unzip it on the computer running the above programs, in the same folder you wish to save your design work. Edit the path to the programs you just installed in 'runRosetta.sh' file, under the 'define variables' section, and you are ready to go. <br>
−
design work. Edit the path to the programs you just installed in 'runRosetta.sh' file, under the 'define variables'  
+
−
section, and you are ready to go. <br>
+
 
<br>
 
<br>
 
<b>Run</b> the main program running the software is <I>'runRosetta.sh'</I>. Run command for initial help:<br>
 
<b>Run</b> the main program running the software is <I>'runRosetta.sh'</I>. Run command for initial help:<br>
−
<br><I>
+
<code> ./runRosetta.sh -h </code> <br>
−
./runRosetta.sh -h <br>
+
The program is divided into steps, according to the steps presented in <b>(1)</b>:<br>
−
<br></I>
+
<b>1. </b> Pre-relax the protein. Run command: <br>
−
The program divided into steps, according to the steps presented in the protocol protocol "Rosetta and the Design of Ligand Binding Sites" <b>(1)</b>:<br>
+
<code>./runRosetta.sh -s 1 -r &lt;receptor file name WITHOUT extension&gt;</code><br>
−
<br>
+
<b>2. </b> Prepare the ligand. Run command: <br>
−
<b>1.</b> Pre-relax the protein. Run command: <br>
+
<code>./runRosetta.sh -s 2 -l &lt;ligand file name WITHOUT extension&gt;</code><br>
−
<br><I>
+
<b>3. </b>Place the ligand into the protein. This is the only step which cannot be done automatically. Follow the instructions at the attached pdf  
−
./runRosetta -s 1 -r &lt;receptor file name WITHOUT extension&gt;<br>
+
file: <a href="https://static.igem.org/mediawiki/2016/2/2d/Step3.3-Ligand_Placement.pdf" >"Step3.3-Place_the_ligand_into_the_protein.pdf"</a><br>
−
<br></I>
+
<b>4. </b>Run Rosetta design. Run command:<br>
−
<b>2.</b> Prepare the ligand. Run command: <br>
+
<code>./runRosetta.sh -s 4 -l &lt;ligand file name WITHOUT extension&gt; -r &lt;receptor file name WITHOUT extension&gt; -m &lt;number of output models&gt; </code><br>
−
<br><I>
+
<b>5. </b>Filter designs. Run command:<br>
−
./runRosetta -s 2 -l &lt;ligand file name WITHOUT extension&gt;.<br>
+
<code>./runRosetta.sh -s 5 </code><br>
−
<br></I>
+
−
<b>3.</b> Place the ligand into the protein. This is the only step cannot be done automatically. Follow the instructions at the attached pdf  
+
−
file: <a href="https://static.igem.org/mediawiki/2016/2/28/Step3.3-Place_the_ligand_into_the_protein.pdf" target="_blank">"Step3.3-Place_the_ligand_into_the_protein.pdf"</a><br>
+
−
<br>
+
−
<b>4.</b>Run Rosetta design. Run command:<br>
+
−
<br><I>
+
−
./runRosetta -s 4 -l &lt;ligand file name WITHOUT extension&gt -r &lt;receptor file name WITHOUT extension&gt -m &lt;number of output models&gt; <br>
+
−
<br></I>
+
−
<b>5.</b>Filter designs. Run command:<br>
+
−
<br><I>
+
−
./runRosetta -s 5 <br>
+
−
<br></I>
+
 
The software offers default filtration, but this is not suitable for any ligand or receptor. The filters can be easily changed in one of the  
 
The software offers default filtration, but this is not suitable for any ligand or receptor. The filters can be easily changed in one of the  
 
files '&lt;results/interfaces&gt;_metrics.config'. To remove a filter just delete it from the config file. To add a filter just add it in the  
 
files '&lt;results/interfaces&gt;_metrics.config'. To remove a filter just delete it from the config file. To add a filter just add it in the  
 
same format as the others in the config file (the column number is the one in the respectively csv score file).<br>
 
same format as the others in the config file (the column number is the one in the respectively csv score file).<br>
−
<br>
+
<b>6. </b> Run new cycle. Run command:<br>
−
<b>6.</b> Run new cycle. Run command:<br>
+
<code>./runRosetta.sh -s 6 -l &lt;ligand file name WITHOUT extension&gt; -r &lt;receptor file name WITHOUT extension&gt; -m &lt;number of output models&gt; </code><br>
−
<br><I>
+
−
./runRosetta -s 6 -l &lt;ligand file name WITHOUT extension&gt; -r &lt;receptor file name WITHOUT extension&gt; -m &lt;number of output <br>
+
−
<br></I>
+
 
For more information see 'README.txt' file in the source zip file.
 
For more information see 'README.txt' file in the source zip file.
 
</p><br>
 
</p><br>
  
−
<br>
 
  
−
<h2>Using online form:</h2>
+
<h2>Using online form</h2>
 
<p class="text-justify">
 
<p class="text-justify">
−
If you do not have access to Linux server, or you just not good with computers, we offer an easy way you can still  
+
If you do not have access to a Linux machine, or simply do not wish to deal with Rosetta, we offer an easy way you can still get your redesigned chemoreceptor. All you need to do is to fill out this form, and we will do the rest. We'll send you the result through the mail in the next few days.<br>
−
get your redesigned ligand binding site. All you need to do is to fill out this form, and we will do the rest. We'll  
+
Note that this is possible only for redesigning the Tar ligand binding domain to bind your desired ligand. If you wish to redesign a different receptor contact us through the mail: technionigem2016@gmail.com.
−
send you the result through the mail in the next few days.<br>
+
−
<br>
+
−
Note that this is possible only for redesigning Tar ligand binding domain to bind your desired ligand. If you wish to  
+
−
redesign different receptor contact us through the mail: technionigem2016@gmail.com
+
 
</p>
 
</p>
 +
<form class="form-horizontal">
 +
<fieldset>
 +
 +
<!-- Text input-->
 +
<div class="form-group">
 +
  <label class="col-md-4 control-label" for="Ligand_name">Ligand Name</label> 
 +
  <div class="col-md-4">
 +
  <input id="Ligand_name" name="Ligand_name" type="text" placeholder="e.g. Aspartate" class="form-control input-md" required="">
 +
   
 +
  </div>
 +
</div>
 +
 +
<!-- Text input-->
 +
<div class="form-group">
 +
  <label class="col-md-4 control-label" for="Full_name">Full Name</label> 
 +
  <div class="col-md-4">
 +
  <input id="Full_name" name="Full_name" type="text" placeholder="john smith" class="form-control input-md" required="">
 +
   
 +
  </div>
 +
</div>
 +
 +
<!-- Text input-->
 +
<div class="form-group">
 +
  <label class="col-md-4 control-label" for="email">Email</label> 
 +
  <div class="col-md-4">
 +
  <input id="email" name="email" type="text" placeholder="123@go.com" class="form-control input-md" required="">
 +
   
 +
  </div>
 +
</div>
 +
 +
<!-- Button -->
 +
<div class="form-group">
 +
  <label class="col-md-4 control-label" for="submit"></label>
 +
  <div class="col-md-4">
 +
    <button id="submit" name="submit" class="btn btn-default" onclick="send()">send</button>
 +
<script>
 +
function send() {
 +
    var email = "technionigem2016@gmail.com";
 +
            var subject = 'Request for online Rosetta design';
 +
            var body = 'Request to run online Rosetta design for:';
 +
var fullname = document.getElementById('Full_name').value;
 +
var ligandname =  document.getElementById('Ligand_name').value;
 +
var returnmail = document.getElementById('email').value;
 +
            document.write('<a href="mailto:' + email + '?subject=' +subject+ '&body=' +body+fullname+ligandname+returnmail '">' + 'Click here to send email as well' + '<'+'/a>');
 +
}
 +
</script>
 +
  </div>
 +
</div>
 +
 +
</fieldset>
 +
</form>
 +
  
 
</div>
 
</div>
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<div class="row">
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<div class="col-sm-10 col-sm-offset-1">
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<div class="col-sm-8 col-sm-offset-2">
−
<a href="#intein_referances" data-toggle="collapse">Referances</a>
+
−
<div id="intein_referances" class="collapse">
+
  
−
<p class="referances">
+
<p class="references">
 +
References:<br>
 
1. Moretti, R., Bender, B.J., Allison, B. and Meiler, J., 2016. Rosetta and the Design of Ligand Binding Sites. Computational Design of Ligand Binding Proteins, pp.47-62.<br>
 
1. Moretti, R., Bender, B.J., Allison, B. and Meiler, J., 2016. Rosetta and the Design of Ligand Binding Sites. Computational Design of Ligand Binding Proteins, pp.47-62.<br>
 
</p>
 
</p>
  
−
</div>
+
 
</div>
 
</div>
 
</div>
 
</div>

Latest revision as of 13:28, 19 October 2016

S.tar, by iGEM Technion 2016

S.tar, by iGEM Technion 2016

Software tool

We worked hard for many months to successfully redesign the ligand binding site of the E. coli Tar chemoreceptor. This feat was done using the Rosetta software suite by following the protocol published by Moretti, R. et al. (1). The work we have achieved can be expanded into other receptors and ligands, and can be of use for other researchers.
Our software tool offers fellow scientists the ability to design their own custom chemoreceptors by redesigning the Tar ligand binding site, and without needing to tackle the many challenges of Rosetta. One can do so in two ways:
1) Using a local installation of Rosetta (preferably on a computer cluster).
2) Online, with the form below.

See the Computational Design page for more explanations about the use of the software, and see the wet lab results of our designs at the results tab.

Using a local installation

We supply a zip file for a Linux system with all necessary scripts to successfully run the redesigning automatically. This script is used only as a framework for working with Rosetta. To successfully run it you are required to download and install the following software: Rosetta, BCL, OpenBabel, Python and a protein visualization program such as UCSF Chimera or PyMol.

Installation: Download our software to Linux operation system and unzip it on the computer running the above programs, in the same folder you wish to save your design work. Edit the path to the programs you just installed in 'runRosetta.sh' file, under the 'define variables' section, and you are ready to go.

Run the main program running the software is 'runRosetta.sh'. Run command for initial help:
./runRosetta.sh -h
The program is divided into steps, according to the steps presented in (1):
1. Pre-relax the protein. Run command:
./runRosetta.sh -s 1 -r <receptor file name WITHOUT extension>
2. Prepare the ligand. Run command:
./runRosetta.sh -s 2 -l <ligand file name WITHOUT extension>
3. Place the ligand into the protein. This is the only step which cannot be done automatically. Follow the instructions at the attached pdf file: "Step3.3-Place_the_ligand_into_the_protein.pdf"
4. Run Rosetta design. Run command:
./runRosetta.sh -s 4 -l <ligand file name WITHOUT extension> -r <receptor file name WITHOUT extension> -m <number of output models>
5. Filter designs. Run command:
./runRosetta.sh -s 5
The software offers default filtration, but this is not suitable for any ligand or receptor. The filters can be easily changed in one of the files '<results/interfaces>_metrics.config'. To remove a filter just delete it from the config file. To add a filter just add it in the same format as the others in the config file (the column number is the one in the respectively csv score file).
6. Run new cycle. Run command:
./runRosetta.sh -s 6 -l <ligand file name WITHOUT extension> -r <receptor file name WITHOUT extension> -m <number of output models>
For more information see 'README.txt' file in the source zip file.


Using online form

If you do not have access to a Linux machine, or simply do not wish to deal with Rosetta, we offer an easy way you can still get your redesigned chemoreceptor. All you need to do is to fill out this form, and we will do the rest. We'll send you the result through the mail in the next few days.
Note that this is possible only for redesigning the Tar ligand binding domain to bind your desired ligand. If you wish to redesign a different receptor contact us through the mail: technionigem2016@gmail.com.


References:
1. Moretti, R., Bender, B.J., Allison, B. and Meiler, J., 2016. Rosetta and the Design of Ligand Binding Sites. Computational Design of Ligand Binding Proteins, pp.47-62.




S.tar, by iGEM Technion 2016