Ligand search tools | IUPHAR/BPS Guide to PHARMACOLOGY

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tools</a> <a href="searchPage.jsp"><img src="images_dev27082012/go.jpg"></a>  <a href="pharmacologySearch.jsp">Pharmacology search tool</a> <a href="pharmacologySearch.jsp"><img src="images_dev27082012/go.jpg"></a></p> <form method="get" action="LigandTextSearchForward"> <fieldset> <h3>Ligand name/text search</h3> <a style="color:white;" href="JavaScript:callRef('helpPagePopup.jsp#ligTextSearch', 800, 400)" title="Click here for help"><img class="logo" style="vertical-align:baseline;" src="images/help_blue_small.png" alt="Click here for help"/></a> <table> <tr> <td align="left" colspan="3" style="padding:10px"> Enter name or text to search: <input type="text" id="ligand_text" size="52" maxlength="300" name="searchString"/> </td> <script> // $("#ligand_text").autocomplete({delay: 300, minLength: 2, source: "autocompleteLigands.jsp"}); $("#ligand_text").autocomplete({delay: 300, minLength: 2, source: "autocompleteLigands.jsp", focus: function( event, ui ) { // $( "#ligand_text" ).val( ui.item.label ); // do nothing on mouse over return false; }, select: function( event, ui ) { //window.open(ui.item.value); self.location.href = ui.item.value; return false; } }); </script> </tr> <tr> <td align="left" style="padding:10px; vertical-align: top;"> Select fields to search: </td> <td align="left" style="padding:10px; vertical-align: top;"> <select name="searchCategories" multiple="true"> <option value="all" selected="selected">All</option> <optgroup label="Ligands"> <option value="ligandName">Name/synonyms</option> <option value="ligandComments">Comments</option> <option value="ligandBioactivity">Bioactivity comments</option> <option value="ligandClinicalUse">Clinical use</option> <option value="ligandMechAction">Mechanism of action</option> <option value="ligandAbsDist">Absorption/distribution</option> <option value="ligandMetabolism">Metabolism</option> <option value="ligandElimination">Elimination</option> <option value="ligandPopnPharmaco">Population pharmacokinetics</option> <option value="ligandOrganFunction">Organ function impairment</option> </optgroup> <optgroup label="Interactions"> <option value="interactionComment">Target-ligand interaction comments</option> <option value="rankPotency">Target rank order of potency</option> </optgroup> <optgroup label="Immunopharmacology"> <option value="ligandImmunoComments">Immunopharmacology Comments</option> <option value="ligandImmunoDisease">Associated Disease</option> <option value="ligandImmunoDiseaseComment">Associated Disease Comments</option> </optgroup> </select> </td> <td align="right" style="padding:10px; vertical-align: top;"> <input type="hidden" name="order" value="rank"/> <input type="submit" name="submitName" value="Search the database"/><br/> </td> </tr> </table> </fieldset> </form> <form method="get" action="LigandTextSearchForward"> <fieldset> <h3>Wildcard name search</h3> <p> Use a wildcard search to match part of a ligand name by adding a <b>% (percent sign)</b> as the wildcard character. </p> <input style="margin-left:10px;" type="text" size="50" maxlength="300" name="searchWildcard"/> <input type="hidden" name="order" value="rank"/> <input type="submit" name="submitWildcard" value="Do wildcard search"/> <p><i>Example: <b>CCL<u>%</u></b> would match <b>CCL<u>3</u></b>, <b>CCL<u>9</u></b> etc.</i></p> </fieldset> </form> <form method="post" action="LigandTextSearchForward"> <a name="idSearch"></a> <fieldset> <h3>Search by chemical identifier</h3> <a style="color:white;" href="JavaScript:callRef('helpPagePopup.jsp#ligIdSearch', 800, 400)" title="Click here for help"><img class="logo" style="vertical-align:baseline;" src="images/help_blue_small.png" alt="Click here for help"/></a> <table> <tr> <td align="left" style="padding:10px"> <label for="idList">Enter identifiers to search: </label> <textarea rows="10" name="searchAcc" id="idList" style="vertical-align: top;"/></textarea> </td> <td style="text-align: center; vertical-align: top; padding:10px;"> Select source: <select name="accTypes"> <option value="binding">BindingDB</option> <option value="cas">CAS Registry No.</option> <option value="chebi">ChEBI</option> <option value="chembl">ChEMBL</option> <option value="drugBank">DrugBank</option> <option value="ensembl">Ensembl</option> <option value="entrezGene">Entrez Gene</option> <option value="hgncId">HGNC Gene Id</option> <option value="hgncName">HGNC Gene Symbol</option> <option value="imgt">IMGT/mAb-DB</option> <option value="iuphar">IUPHAR/BPS GtoPdb Ligand Id</option> <option value="mgiId">MGI Gene Id</option> <option value="mgiName">MGI Gene Symbol</option> <option value="nursa">NURSA Ligand Id</option> <option value="omim">OMIM</option> <option value="pubchemCid" selected="selected">PubChem CID</option> <option value="pdb">PDB Code/Ligand Id</option>--%> <option value="RefSeqP">RefSeq Protein</option> <option value="rgdId">RGD Gene Id</option> <option value="rgdName">RGD Gene Symbol</option> <option value="inchi">Standard InChI</option> <option value="inchiKey">Standard InChI Key</option> <option value="uniparc">UniParc</option> <option value="uniProt">UniProt</option> <option value="none">Unknown</option> </select> <br/> <br/> <input type="hidden" name="order" value="rank"/> <input type="submit" name="submitAcc" value="Search the database"/><br/> </td> </tr> <tr> <td style="text-align: left; padding:0px 10px;" colspan="2"> <div id="file_upload" style="margin-bottom: 10px;"> <label for="file">Or upload a file: </label> <input type="file" onchange="fileUploaded(event);" id="file"></input> </div> <small><a href="#idSearch" onclick="clearIds();">Clear</a></small> </td> </tr> </table> </fieldset> </form> <form method="get" action="LigandTextSearchForward"> <fieldset> <h3>Search for data by literature reference</h3> <a style="color:white;" href="JavaScript:callRef('helpPagePopup.jsp#ligRefSearch', 800, 400)" title="Click here for help"><img class="logo" style="vertical-align:baseline;" src="images/help_blue_small.png" alt="Click here for help"/></a> <table cellpadding="10"> <tr> <td align="left" colspan="2"> Enter title keyword, author name or PubMed Id: <input type="text" size="36" maxlength="100" name="searchRef"/> </td> </tr> <tr> <td align="left"> Select field to search: <select name="refField"> <option value="refTitle">Title</option> <option value="refAuthor">Author</option> <option value="refPMID">PubMed Id</option> </select> </td> <td align="right"> <input type="hidden" name="order" value="rank"/> <input type="submit" name="submitRef" value="Search the database"/><br/> </td> </tr> </table> </fieldset> </form> <div id="chemicalize_search"> <div id="chemicalize_sketch"> <a name="structureSearch"></a><h3>Chemical structure search</h3> <a style="color:white;" href="JavaScript:callRef('helpPagePopup.jsp#ligStructureSearch', 800, 400)" title="Click here for help"><img class="logo" style="vertical-align:baseline;" src="images/help_blue_small.png" alt="Click here for help"/></a> <table> <tr> <td valign="top" style="padding:0px 10px 0px 10px;" colspan="2"> <p style="font-size:105%;font-weight:bold;">1. Load or draw a structure into the editor below</p> <p align="left"> <INPUT id="insmi" type="text" name="insmi" size=45" > <button ID="inputy" type="button">Import SMILES</button> </p> <p> If the SMILES does not display after clicking 'Import SMILES' try importing directly on the MarvinJS sketch tool. Click the second from left icon on the top row (or use ctrl-O). Importing in this way will give an error if the SMILES is invalid. </p> <p> To return all relevant hits please ensure that your input structure <b>does not</b> include chiral specification. </p> </td> </tr> </table> <div id="marvintest" style="width: 700px; height: 480px"></div> <table><tr> <td style="text-align:left;vertical-align:top;"> <a style="color:white;" href="http://www.chemaxon.com/" target="_blank"><img class="logo" src="images/powered_by_chemaxon.png" alt="ChemAxon"/></a> </td> <td style="text-align:center;vertical-align:top;"> <small><a href="https://pro.chemicalize.com/" target="_blank">Chemicalize Pro</a></small> </td> <td style="text-align:right;vertical-align:top;"> <small><a href="http://www.daylight.com/dayhtml_tutorials/languages/smarts/index.html" target="_blank">SMARTS help</a></small> </td> </tr> </table> <table> <tr> <td align="left" valign="top" style="padding:10px"> <p style="font-size:105%;font-weight:bold;">2. Choose type of search to perform <select id="searchtype" name="type"> <option value="exact">Exact</option> <option value="substruct" selected="selected">Substructure</option> <option value="similarHigh">Similarity: high (>85%)</option> <option value="similarMod">Similarity: moderate (>70%)</option> <option value="smarts">SMARTS</option> </select> </p> <p style="font-size:105%;font-weight:bold;">3. Limit results by chemical class <select id="ligtype" name="ligclass"> <option value="SmallMol" selected="selected">Small molecules</option> <option value="Peptide">Peptides</option> </select> <br> </p> </td></tr></table> <p id="marvinlog"></p>  <button id="sendy" type="button">Search Database</button>  <script> ChemicalizeMarvinJs.createEditor('#marvintest').then(function(marvin) { function handleMolChange() { marvin.exportStructure('smiles').then(function(smiles) { document.getElementById('marvinlog').innerHTML = 'Molecule has been changed to: ' + smiles; }); } function showDialog() { marvin.exportStructure('smiles').then(function(smiles) { alert("Current molecule: " + smiles); }); } function sendForm() { var type = document.getElementById('searchtype').value; var ligclass = document.getElementById('ligtype').value; marvin.exportStructure('smiles').then(function(smiles) { if(smiles == null || smiles == ""){ alert("No input structure to search for!"); return; } smiles = smiles.replace(/=/g,"%3D"); smiles = smiles.replace(/#/g,"%23"); //alert("Current molecule: " + type +" " +ligclass +" "+smiles); //window.location.href = "ChemicalStructureSearchForward?smi="+smiles+"&type="+type+"&ligclass="+ligclass, '_blank'; // //Feb 24: set URL and send reuslt to new tab - preserving the query window so user can more easily refine query. var url = "ChemicalStructureSearchForward?smi="+smiles+"&type="+type+"&ligclass="+ligclass; window.open(url, "_blank"); }); } function loadSketch(){ var in_smi = document.getElementById('insmi').value; if(in_smi == null || in_smi == ""){ alert("No input structure provided!"); return; } if(in_smi != null || in_smi != ""){ alert("Structure found to load: "+ in_smi); try { marvin.importStructure('smiles', in_smi); } catch(err) { alert("SMILES may not be valid: " + smiles +" |ERROR: "+err); } } //marvin.importStructure('name', 'benzene'); } marvin.on('molchange', handleMolChange); //document.getElementById('actionbutton').addEventListener("click", showDialog); 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