516 lines
23 KiB
HTML
516 lines
23 KiB
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<div class="row">
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<a href="/research/mutabind2/" ><img src="/projects/mutabind/prj-sunddg/static/myimgs/CirclesDiamondBlueThiner.png" style="height:70px;width:auto;margin-top: 0.2rem;" /></a>
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<a href="/research/mutabind2/" ><img src="/projects/mutabind/prj-sunddg/static/myimgs/TitleBlues.png" style="height:70px;width:auto" /></a>
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<div class="row">
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<div class="small-7 small-centered columns" style="text-align:center;position:relative;z-index:999">
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<h5 class="text-center subheader"> Predicting Binding Affinity Changes upon Mutation </h5>
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<div class="small-5 columns" style="padding-left:0;text-align:center;position:relative;z-index:999">
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<h3 class="text-left subheader" style="font-weight:700"> Predicting Binding Affinity<br> Changes upon Mutation </h3>
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<!--Content here-->
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<p class="text-justify"><strong>MutaBind2</strong> evaluates the effects of mutations on protein-protein interactions for soluble complexes. It calculates changes in binding affinity upon single or multiple mutations and provides a structural model of mutated complex. The structure of a protein-protein complex is required for this method. MutaBind2 is the second version of MutaBind method. <span style="color: #FF0000">The method can be used for SARS-CoV-2 modeling.</span></p>
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<style>
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h6.left {
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margin-right:1rem;
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display:block;
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}
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.subindex
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{
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vertical-align:sub;
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font-size:60%;
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}
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</style>
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<div class="row">
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<div class="small-12 small-centered columns">
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<a href="/research/mutabind2/method"><img src="/projects/mutabind/prj-sunddg/static/myimgs/Complex4.png" alt="Complex4" /></a>
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</div>
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</div>
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<br>
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<hr>
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<h3> Step 1 - Select Protein Complex </h3>
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<br>
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<form action="/research/mutabind2/upload_pdb" method="post" id="pdb_form" enctype="multipart/form-data">
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<input type='hidden' name='csrfmiddlewaretoken' value='zbvPVhYnoKwy17n6NBHUgSxYcfveLHof' />
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<input type="hidden" id="example" name="example" value="0">
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<input type="hidden" id="pdb_container_asu" name="pdb_container_asu" value="">
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<input type="hidden" id="pdb_container_bio" name="pdb_container_bio" value="">
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<input type="hidden" id="isNMR" name="isNMR" value="0">
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<div class="row">
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<div class="small-3 columns">
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<label for="pdb_id_input" class="left" style="font-size:1.3rem">Input PDB code:</label>
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</div>
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<div class="small-3 columns">
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<input type="text" id="pdb_id_input" name="pdb_id" style="margin-bottom:0.5rem" placeholder="PDB id code [4-letter code]" class="radius" />
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<span class="subheader"> Example: <a id="load_example">1CSE</a></span>
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</div>
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<div class="small-1 columns">
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<div class="switch radius small ">
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<input id="pdb_bio" type="radio" checked name="pdb_mol" value="bio">
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<label for="pdb_bio"></label>
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</div>
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<div class="switch radius small ">
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<input id="pdb_asu" type="radio" name="pdb_mol" value="asu">
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<label for="pdb_asu"></label>
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</div>
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</div>
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<div class="small-1 columns">
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<select id="bioassemblies" name="bioassembly" style="margin:0;height: 2em;padding: 0;width: 3.4em;">
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<option value="1">1st</option>
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</select>
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</div>
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<div class="small-4 columns" style="padding-left:0">
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<h6 class="">Bioassembly <span data-tooltip data-options="width:300" aria-haspopup="true" class="has-tip radius" title="For multiple bioassemblies, default bioassembly will be used (.pdb1)"><i class="fi-info small"></i></span></h6>
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<h6 class="left">Asymmetric Unit</h6>
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</div>
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<!--<div class="small-3 end columns">-->
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<!--<p>Asymetric Unit </p>-->
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<!--<p>Bioassembly</p>-->
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<!--</div>-->
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</div>
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<div class="row">
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<div class="small-5 small-offset-7 columns end">
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<div id="nmr_warning" style="font-size:0.8rem;color:red"></div>
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</div>
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</div>
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<div class="row">
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<div class="small-12 columns" >
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<div id="pdb_description"></div>
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</div>
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</div>
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<div class="row">
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<div class="small-12 columns" >
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<div id="large_warning"></div>
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</div>
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</div>
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<div class="row">
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<div data-alert class="small-12 columns">
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<div id="pdb_warning" data-alert class="small-12 columns">
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<!-- <p id="pdb_warning"></p> -->
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</div>
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</div>
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</div>
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<hr>
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<div class="row">
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<div class="small-3 columns">
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<label for="pdb_file_input" class="left" style="font-size:1.3rem">Upload PDB file:</label>
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</div>
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<div class="small-6 columns">
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<input type="file" id="pdb_file_input" name="pdb_file" class="radius" onchange="fileChange(this);"/>
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</div>
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</div>
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<div class="row">
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<div class="small-6 columns">
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<label style="font-size:1.1rem">Format description <span data-tooltip data-options="width:300" aria-haspopup="true" class="has-tip radius" title="Uploaded file should follow the standard PDB format. If uploaded file includes multiple models (ex: bio-assembly or NMR structures), please make sure that file does not contain 'MODEL' tags (as used in PDB bioassembly files) and does not contain duplicated chain identifiers. Chain identifier should only use upper and lower-case letters."><i class="fi-info small"></i></span> for uploaded file</label>
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</div>
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</div>
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<div id="manually_info" class="row" style="margin-top: 10px;display:none;">
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<!--
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<div class="small-10 columns">
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<div data-alert class="alert-box warning">
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If your PDB file cannot be loaded, please download it from the RCSB PDB and upload it manually.
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</div>
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</div>
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-->
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<div class="small-12 columns">
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<label style="font-size:1.1rem;color: #FF0000">If your PDB file cannot be loaded, please download it from the RCSB PDB and upload it manually.</label>
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</div>
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</div>
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<hr>
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<div class="row">
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<!--<div class="large-12 columns" >
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<label style="font-size:1.1rem">Additional Options</label>
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<input id="isPI" type="checkbox" name="isPI" value="isPI"><label style="font-size:1.1rem" for="isPI">Is protease-inhibitor complex? <span data-tooltip data-options="width:300" aria-haspopup="true" class="has-tip radius" title="This is a special model that gives better predictions for protease inhibitor complexes. Check this box if you want to use it."><i class="fi-info small"></i></span></label>
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<button cccc="event.preventDefault(); alert('MutaGene will not be able to run new jobs until May 7th due to server maintenance');" type="submit" class="button radius right" id="submit_button">Next</button>-->
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<div class="large-6 large-offset-3 columns" >
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<button cccc="event.preventDefault(); alert('MutaGene will not be able to run new jobs until May 7th due to server maintenance');" type="submit" class="button radius left" id="single">Single Mutation</button>
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<button cccc="event.preventDefault(); alert('MutaGene will not be able to run new jobs until May 7th due to server maintenance');" type="submit" class="button radius right" id="multiple">Multiple Mutation</button>
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<input id="mutationType" type="hidden" name="type" value="0">
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</div>
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</div>
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<div class="row">
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<div id="console" data-alert class="small-12 columns"></div>
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</div>
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<div class="row">
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<div data-alert class="small-12 columns">
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<div id="upload_warning" data-alert class="small-12 columns">
|
||
<!-- <p id="pdb_warning"></p> -->
|
||
</div>
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||
</div>
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||
</div>
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</form>
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|
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<div class="notifications top-right"></div>
|
||
<script>
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||
function manually_notice() {
|
||
// body...
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$("#manually_info").show('fast');
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||
}
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$(document).foundation();
|
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$(document).ready(function(){
|
||
//alert('Our server is not available from 5:00 p.m. to 7:00 a.m. Beijing time until Oct. 24.');
|
||
//$('.top-right').notify({
|
||
// type:'info',
|
||
// transition:'fade',
|
||
// message: {text: 'Our server is not available from 5:00 p.m. to 7:00 a.m. Beijing time until Oct. 24.'},
|
||
// fadeOut:{enabled: true, delay: 20000}
|
||
//}).show();
|
||
$("#single").on('click', function(){
|
||
$("#console").append("<div id=\"loading_message\" data-alert class=\"alert-box secondary radius\"> <img src=\"/projects/mutabind/prj-sunddg/static/myimgs/ajax-loader.gif\" /> Uploading data ... This may take a few seconds </div>");
|
||
$("#pdb_form").submit();
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console.log('single');
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||
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||
//setTimeout("manually_notice()", 20000 )
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||
|
||
});
|
||
$("#multiple").on('click', function(){
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||
$("#console").append("<div id=\"loading_message\" data-alert class=\"alert-box secondary radius\"> <img src=\"/projects/mutabind/prj-sunddg/static/myimgs/ajax-loader.gif\" /> Uploading data ... This may take a few seconds </div>");
|
||
$("#mutationType").val("1");
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$("#pdb_form").submit();
|
||
console.log('multiple');
|
||
//setTimeout("manually_notice()", 20000 )
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||
});
|
||
/*
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||
$("#submit_button").on('click', function(){
|
||
$("#console").append("<div id=\"loading_message\" data-alert class=\"alert-box secondary radius\"> <img src=\"/projects/mutabind/prj-sunddg/static/myimgs/ajax-loader.gif\" /> Uploading data ... This may take a few seconds </div>");
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||
})
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||
*/
|
||
/*
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||
$("#single").on('click', function(){
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||
$("#console").append("<div id=\"loading_message\" data-alert class=\"alert-box secondary radius\"> <img src=\"/projects/mutabind/prj-sunddg/static/myimgs/ajax-loader.gif\" /> Uploading data ... This may take a few seconds </div>");
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||
if ($('#pdb_file_input').get(0).files.length != 0) {
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||
// there is a file, use it
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return true; // submit
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}
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var asu_url = "//files.rcsb.org/download/" + $("#pdb_id_input").val().toUpperCase() + ".pdb";
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var bio_url = "//files.rcsb.org/download/" + $("#pdb_id_input").val().toUpperCase() + ".pdb" + $("#bioassemblies").val();
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var bio_alternative_url = asu_url;
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$.when(
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$.get(asu_url, function(data) {
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$("#pdb_container_asu").val(data);
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}, dataType="text"),
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$.get(bio_url, function(data) {
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$("#pdb_container_bio").val(data);
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}, dataType="text").then(function(){}, function(){
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return $.get(bio_alternative_url, function(data) {
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$("#pdb_container_bio").val(data);
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}, dataType="text");
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})
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||
).then(function() {
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||
//ok, we loaded pdb. submit the form
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||
//console.log($("#pdb_container_asu").val());
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||
//console.log($("#pdb_container_bio").val());
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||
|
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$("#pdb_form").submit();
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||
}, function() {
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||
// error message:
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||
$("#loading_message").remove();
|
||
var warning = "One of the files for selected PDB entry could not be received from the RCSB website";
|
||
$("#pdb_warning").css("display", "none")
|
||
.addClass("alert alert-box radius")
|
||
.text(warning)
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||
.fadeIn("fast");
|
||
});
|
||
return false; // do not submit
|
||
});
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||
|
||
$("#multiple").on('click', function(){
|
||
$("#console").append("<div id=\"loading_message\" data-alert class=\"alert-box secondary radius\"> <img src=\"/projects/mutabind/prj-sunddg/static/myimgs/ajax-loader.gif\" /> Uploading data ... This may take a few seconds </div>");
|
||
|
||
if ($('#pdb_file_input').get(0).files.length != 0) {
|
||
$("#mutationType").val("1");
|
||
$("#pdb_form").submit();
|
||
// there is a file, use it
|
||
return false; // submit
|
||
}
|
||
|
||
var asu_url = "//files.rcsb.org/download/" + $("#pdb_id_input").val().toUpperCase() + ".pdb";
|
||
var bio_url = "//files.rcsb.org/download/" + $("#pdb_id_input").val().toUpperCase() + ".pdb" + $("#bioassemblies").val();
|
||
var bio_alternative_url = asu_url;
|
||
|
||
$.when(
|
||
$.get(asu_url, function(data) {
|
||
$("#pdb_container_asu").val(data);
|
||
}, dataType="text"),
|
||
|
||
$.get(bio_url, function(data) {
|
||
$("#pdb_container_bio").val(data);
|
||
}, dataType="text").then(function(){}, function(){
|
||
return $.get(bio_alternative_url, function(data) {
|
||
$("#pdb_container_bio").val(data);
|
||
}, dataType="text");
|
||
})
|
||
).then(function() {
|
||
//ok, we loaded pdb. submit the form
|
||
//console.log($("#pdb_container_asu").val());
|
||
//console.log($("#pdb_container_bio").val());
|
||
|
||
//change the attribute type's value to 1, it means multiple mutation
|
||
//added by gavin
|
||
$("#mutationType").val("1");
|
||
|
||
$("#pdb_form").submit();
|
||
}, function() {
|
||
// error message:
|
||
$("#loading_message").remove();
|
||
var warning = "One of the files for selected PDB entry could not be received from the RCSB website";
|
||
$("#pdb_warning").css("display", "none")
|
||
.addClass("alert alert-box radius")
|
||
.text(warning)
|
||
.fadeIn("fast");
|
||
});
|
||
return false; // do not submit
|
||
});
|
||
|
||
*/
|
||
$("#load_example").click(function(){
|
||
$("#pdb_id_input").val("1CSE")
|
||
$("#example").val("1")
|
||
$("#pdb_id_input").trigger("propertychange")
|
||
return false;
|
||
})
|
||
|
||
});
|
||
</script>
|
||
<script>
|
||
|
||
function fileChange(target) {
|
||
|
||
var name=target.value;
|
||
var fileName = name.substring(name.lastIndexOf(".")+1).toLowerCase();
|
||
//console.log(fileName.substring(0,3).toLowerCase());
|
||
//console.log(Number( fileName.substring(3,)));
|
||
$("#upload_warning").css("display", "none");
|
||
|
||
if(fileName.substring(0,3).toLowerCase() !="pdb" || isNaN(Number( fileName.substring(3,)))){
|
||
$("#loading_message").remove();
|
||
//var warning = "One of the files for selected PDB entry could not be received from the RCSB website";
|
||
var warning = " Uploaded file must be a standard PDB format!"
|
||
$("#upload_warning").css("display", "none")
|
||
.addClass("alert alert-box radius")
|
||
.text(warning)
|
||
.fadeIn("fast");
|
||
target.value="";
|
||
return false; //can not submit
|
||
|
||
}
|
||
|
||
}
|
||
|
||
|
||
</script>
|
||
|
||
<div class="row">
|
||
<div class="small-12 columns">
|
||
<p style="margin:0;"><strong>Reference</strong></p>
|
||
|
||
<p style="line-height:1.2;font-size: 0.9rem;color: black;">Zhang N, Chen Y, Lu H, Zhao F, Alvarez RV, Goncearenco A, Panchenko AR, Li M. <i> MutaBind2: Predicting the Impacts of Single and Multiple Mutations on Protein-Protein Interactions.</i><strong> iScience. PMID:</strong><a href="https://pubmed.ncbi.nlm.nih.gov/32169820/" style="font-size: 0.9rem;"> 32169820</a></p>
|
||
<!--
|
||
<p style="line-height:1.2;font-size: 0.9rem;color: black;">Li M, Simonetti FL, Goncearenco A & Panchenko AR. <i> MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions.</i><strong> Nucleic Acids Res. (2016 Web Server Issue). PMID:</strong><a href="//www.ncbi.nlm.nih.gov/pubmed/?term=MutaBind+estimates+and+interprets+the+effects+of+sequence+variants+on+protein%E2%80%93protein+interactions" style="font-size: 0.9rem;"> 27150810</a></p>
|
||
-->
|
||
</div>
|
||
</div>
|
||
|
||
<script>
|
||
var _hmt = _hmt || [];
|
||
(function() {
|
||
var hm = document.createElement("script");
|
||
hm.src = "https://hm.baidu.com/hm.js?f3c51068660488e0335a08348130b6ee";
|
||
var s = document.getElementsByTagName("script")[0];
|
||
s.parentNode.insertBefore(hm, s);
|
||
})();
|
||
</script>
|
||
|
||
|
||
</div>
|
||
</div>
|
||
|
||
<div class="row">
|
||
<div class="small-12 column">
|
||
<hr>
|
||
<!--
|
||
<a target="_blank" href="//www.ncbi.nlm.nih.gov/" ><img src="/projects/mutabind/prj-sunddg/static/myimgs/white_ncbi.png" class="left" style="width:27px;height:auto;margin-right:10px"/></a>
|
||
<a target="_blank" href="//www.nih.gov/" ><img src="/projects/mutabind/prj-sunddg/static/myimgs/NIH_NLM.png" class="left" style="width:120px;height:auto"/></a>
|
||
|
||
-->
|
||
|
||
<div class="small-6 column">
|
||
<h6 style="line-height:15.5px;"><small>School of Biology & Basic Medical Sciences, Soochow University<br>199 Ren-Ai Road, Suzhou, Jiangsu, 215123 P.R. China</small></h6>
|
||
</div>
|
||
|
||
<a href="https://lilab.jysw.suda.edu.cn/#/contact" class="right">Contact Us </a>
|
||
</div>
|
||
</div>
|