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Modified Nucleotides

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The table can be filtered by Parent NT, by modification location (base, sugar, and/or phosphate), by chirality change present (e.g., base, 2'OH, 3'OH or 5'C position change from below/above sugar ring, or phosphate location change), and by designation of full racemate of the Parent. Click on the non-standard nucleotide PDB chemical component dictionary id (_ccdid_) to view its full description at RCSB.org. Turn on atom mapping details to see change details in terms of atom additions, deletions, and substitutions. <a href="https://rna.bgsu.edu/modified/modified_to_change_data.json" target="_blank">View/Download raw data file (json)</a>. Comments/Questions/Corrections? -- please let us know at <a href="mailto:help@nakb.org">help@nakb.org</a>.</p> <a id="reset" class="btn btn-sm" style="background-color: #333399; color: white; " onclick="reset()">Reset All</a> <br/> <br/> <table class="table"> <tr><td> <b>Filter by Parent NT</b></td><td> <form onchange=on_select()> <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="all" name="radiont" value="*" checked="checked"> <label class="custom-control-label" for="all">Show All</label> </div> &nbsp;<b>DNA:</b>&nbsp; <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="da" name="radiont" value="DA"> <label class="custom-control-label" for="da">DA</label> </div> <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="dc" name="radiont" value="DC"> <label class="custom-control-label" for="dc">DC</label> </div> <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="dg" name="radiont" value="DG"> <label class="custom-control-label" for="dg">DG</label> </div> <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="dt" name="radiont" value="DT"> <label class="custom-control-label" for="dt">DT</label> </div> &nbsp;<b>RNA:</b>&nbsp; <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="ra" name="radiont" value="A"> <label class="custom-control-label" for="ra">A</label> </div> <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="rc" name="radiont" value="C"> <label class="custom-control-label" for="rc">C</label> </div> <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="rg" name="radiont" value="G"> <label class="custom-control-label" for="rg">G</label> </div> <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="ru" name="radiont" value="U"> <label class="custom-control-label" for="ru">U</label> </div> &nbsp;<b>Mapping Status:</b>&nbsp; <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="any" name="radiont" value="mapped"> <label class="custom-control-label" for="any">Any Parent</label> </div> <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="unmapped" name="radiont" value="unmapped"> <label class="custom-control-label" for="unmapped">Unmapped</label> </div> </form> </td></tr> <tr><td> <b>Filter by Modification Location</b></td><td> <form onchange=on_select()> <b>Base:</b>&nbsp; <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="baseincl" name="radiobase" value="1" > <label class="custom-control-label" for="baseincl">+</label> </div> <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="baseomit" name="radiobase" value="0"> <label class="custom-control-label" for="baseomit">-</label> </div> <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="baseany" name="radiobase" value="100" checked="checked"></div> <b>Sugar:</b>&nbsp; <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="sugarincl" name="radiosugar" value="1" > <label class="custom-control-label" for="sugarincl">+</label> </div> <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="sugaromit" name="radiosugar" value="0"> <label class="custom-control-label" for="sugaromit">-</label> </div> <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="sugarany" name="radiosugar" value="100" checked="checked"></div> <b>Phosphate:</b>&nbsp; <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="phosincl" name="radiophos" value="1" > <label class="custom-control-label" for="phosincl">+</label> </div> <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="phosomit" name="radiophos" value="0"> <label class="custom-control-label" for="phosomit">-</label> </div> <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="phosany" name="radiophos" value="100" checked="checked"></div> </form> </td></tr> <tr><td> <b>Filter by Modification Type</b></td><td> <form onchange=on_select()> <b>Chirality:</b>&nbsp; <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="chiralincl" name="radiochiral" value="1" > <label class="custom-control-label" for="chiralincl">+</label> </div> <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="chiralomit" name="radiochiral" value="0"> <label class="custom-control-label" for="chiralomit">-</label> </div> <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="chiralany" name="radiochiral" value="100" checked="checked"></div> <b>Full Racemate:</b>&nbsp; <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="racemateincl" name="radioracemate" value="1" > <label class="custom-control-label" for="racemateincl">+</label> </div> <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="racemateomit" name="radioracemate" value="0"> <label class="custom-control-label" for="racemateomit">-</label> </div> <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="racemateany" name="radioracemate" value="100" checked="checked"></div> </form> </td></tr> <tr><td> <b>Image Type</b></td><td> <form onchange=on_select()> <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="imagercsb" name="radioimage" value="RCSB" checked="checked"> <label class="custom-control-label" for="imagercsb">RCSB</label> </div> <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="imagebase" name="radioimage" value="Base"> <label class="custom-control-label" for="imagebase">Base</label> </div> <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="imagefull" name="radioimage" value="Full"> <label class="custom-control-label" for="imagefull">Full</label> </div> </form> </td></tr> <tr><td> <b>Show Atom Mapping Details</b></td><td> <form onchange=on_select()> <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="detailsyes" name="showdetails" value="1"> <label class="custom-control-label" for="detailsyes">+</label> </div> <div class="custom-control custom-radio custom-control-inline"> <input type="radio" class="custom-control-input" id="detailsno" name="showdetails" value="0" checked="checked"> <label class="custom-control-label" for="detailsno">-</label> </div> </form> </td></tr> </table> <br/> <div id="results"> </div> <div id="test"></div> <div id="sourcetable"></div> </div> </div> </div> <!--end overall panel body--> <footer class="page-footer"> <div class="container-fluid"> <div class="row" style="color:#FFF; 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window.open(url); } else if (results2 !== null) { url = "/atlas=" + searchInput.toUpperCase(); window.open(url); } else { url = "/?nakblist=" + searchInput; window.open(url); } } }); </script> </body> <script> const ntname= { "A": "adenosine-5'-monophosphate", "C": "cytosine-5'-monophosphate", "G": "guanosine-5'-monophosphate", "U": "uridine-5'-monophosphate", "DA": "2'-deoxyadenosine-5'-monophosphate", "DC": "2'-deoxycytosine-5'-monophosphate", "DG": "2'-deoxyguanosine-5'-monophosphate", "DT": "thymidine-5'-monophosphate"}; var searchvar = ""; var urlregex = new RegExp( "[?].+" ); var urlresults = urlregex.exec( window.location.href ); if ( urlresults !== null ) { searchvar = urlresults[0].slice(1); } on_select(); function getcounts(simplearray) { simplearray.sort(); let simplearraycount = {}; for (let z in simplearray) { if (!simplearraycount[simplearray[z]]) { simplearraycount[simplearray[z]] = 0;} ++simplearraycount[simplearray[z]]; } let simplearraytxt = []; //for (z in simplearraycount) {simplearraytxt.push( z + "(" + simplearraycount[z] + ")"); } for (z in simplearraycount) {simplearraytxt.push(z); } return simplearraytxt; } function on_select(){ const getjson = new XMLHttpRequest(); getjson.onload = function() {const ntMods = JSON.parse(this.responseText); var filtstdnt= $('input[name="radiont"]:checked').val(); let inclbase= $('input[name="radiobase"]:checked').val(); let inclsuga= $('input[name="radiosugar"]:checked').val(); let inclphos= $('input[name="radiophos"]:checked').val(); let inclchir= $('input[name="radiochiral"]:checked').val(); let inclracm= $('input[name="radioracemate"]:checked').val(); let incladdi=100 let incladbo=100 let inclrepl=100 let inclremo=100 let imagetype= $('input[name="radioimage"]:checked').val(); //let imagetype= "RCSB"; let detailstoggle = $('input[name="showdetails"]:checked').val(); let text = "<table class='table table-sm' id='sort' style='width:100%'><thead><tr> <th style='width:35%' scope='col'>Parent NT</th><th style='width:35%' scope='col'>Modified NT</th><th scope='col'>Modification Location(s)</th>" + "<th scope='col'>Modified NT Atom Count</th>" ; if (detailstoggle == 1) { text += "<th scope='col'>Atom Mapping Details</th>" ; } text += "<th scope='col'>#NAKB entries</th></tr></thead> <tbody>"; for (let x in ntMods) { let stdnt = ntMods[x].standard_base[0]; //run through filter conditions if (filtstdnt != "mapped" && filtstdnt != "unmapped") { if (filtstdnt != "*" && stdnt != filtstdnt ) {continue;} } else if (ntMods[x].standard_base.length == 0 && filtstdnt=="mapped") {continue;} else if (ntMods[x].standard_base.length > 0 && filtstdnt=="unmapped") {continue;} //process change info for next set of filters let changeloc=[]; for (let y in ntMods[x].changes) { changeloc.push(ntMods[x].changes[y].change_location); } let loctxt= getcounts(changeloc).join(", ") ; let changetype=[]; for (let y in ntMods[x].changes) { changetype.push(ntMods[x].changes[y].change_type); } let typtxt= getcounts(changetype).join(" ") ; if (inclbase==0 && loctxt.search("base")>-1) {continue;} if (inclbase==1 && loctxt.search("base")==-1) {continue;} if (inclsuga==0 && loctxt.search("ribose")>-1) {continue;} if (inclsuga==1 && loctxt.search("ribose")==-1) {continue;} if (inclphos==0 && loctxt.search("phosphate")>-1) {continue;} if (inclphos==1 && loctxt.search("phosphate")==-1) {continue;} if (inclchir==0 && typtxt.search("over_under")>-1) {continue;} if (inclchir==1 && typtxt.search("over_under")==-1) {continue;} if (inclracm==0 && typtxt.search("chirality_reversal")>-1) {continue;} if (inclracm==1 && typtxt.search("chirality_reversal")==-1) {continue;} /*if (inclremo==0 && typtxt.search("removal")>-1) {continue;} if (inclremo==1 && typtxt.search("removal")==-1) {continue;} if (incladdi==0 && typtxt.search("addition")>-1) {continue;} if (incladdi==1 && typtxt.search("addition")==-1) {continue;} if (incladbo==0 && typtxt.search("added_bond")>-1) {continue;} if (incladbo==1 && typtxt.search("added_bond")==-1) {continue;} if (inclrepl==0 && typtxt.search("replacement")>-1) {continue;} if (inclrepl==1 && typtxt.search("replacement")==-1) {continue;} */ text += "<tr><td>"; //standard NT if (ntMods[x].standard_base.length > 0) { text += "<a href='https://rcsb.org/ligand/" + stdnt + "' target='_blank' >" + stdnt + "</a><br/>"; if (imagetype == "RCSB") { let stdstem = stdnt.substring(0,1) + "/"; text += "<img style='height: 350px;' src='https://cdn.rcsb.org/images/ccd/labeled/" + stdstem + stdnt + ".svg'>"; } else if (imagetype == "Base") { text += "<img style='height: 350px;' src='https://rna.bgsu.edu/modified/img/base_" + stdnt + "_" + stdnt + ".gif'>"; } else if (imagetype == "Full") { text += "<img style='height: 350px;' src='https://rna.bgsu.edu/modified/img/backbone_" + stdnt + "_" + stdnt + ".gif'>"; } text += "<br/>" + ntname[stdnt] ; } else {text += "Not Mapped";} text += "</td><td>"; //modified NT text += "<a href='https://rcsb.org/ligand/" + x + "' target='_blank' >" + x + "</a><br/>"; if (imagetype == "RCSB") { let xstem = x.substring(0,1) + "/"; text += "<img style='height: 350px;' src='https://cdn.rcsb.org/images/ccd/labeled/" + xstem + x + ".svg'>"; } else if (imagetype == "Base") { text += "<img style='height: 350px;' src='https://rna.bgsu.edu/modified/img/base_" + stdnt + "_" + x + ".gif'>"; } else if (imagetype == "Full") { text += "<img style='height: 350px;' src='https://rna.bgsu.edu/modified/img/backbone_" + stdnt + "_" + x + ".gif'>"; } text += "<br/>" + ntMods[x].pdb.name ; text += "</td><td>" + loctxt + "<br/><span style='color:white'>_" + x + "_</td>"; //whited-out ligand id with "_" padding for exact filtering let chgtxt = "<ul>"; if (ntMods[x].changes.length > 0) { for (let y in ntMods[x].changes) { if (ntMods[x].changes[y].change_type == "addition") { chgtxt += "<li>" + ntMods[x].changes[y].modified_atom + "(" + ntMods[x].changes[y].modified_element + ")" + "==>" + ntMods[x].changes[y].new_modified_atom + "(" + ntMods[x].changes[y].new_modified_element + ")" + "|" + ntMods[x].changes[y].change_type + "|" + ntMods[x].changes[y].change_location + "</li>";} else if (ntMods[x].changes[y].change_type == "added_bond") { chgtxt += "<li>" + ntMods[x].changes[y].parent_atom_1 + "--" + ntMods[x].changes[y].parent_atom_2 + "<=>" + ntMods[x].changes[y].modified_atom_1 + "--" + ntMods[x].changes[y].modified_atom_2 + "|" + ntMods[x].changes[y].change_type + "|" + ntMods[x].changes[y].change_location + "</li>";} else if (ntMods[x].changes[y].change_type == "replacement") { chgtxt += "<li>" + ntMods[x].changes[y].parent_atom + "(" + ntMods[x].changes[y].parent_element + ")" + "<=>" + ntMods[x].changes[y].modified_atom + "(" + ntMods[x].changes[y].modified_element + ")" + "|" + ntMods[x].changes[y].change_type + "|" + ntMods[x].changes[y].change_location + "</li>";} else if (ntMods[x].changes[y].change_type == "removal") { chgtxt += "<li>" + ntMods[x].changes[y].parent_atom + "(" + ntMods[x].changes[y].parent_element + ")|" + ntMods[x].changes[y].change_type + "|" + ntMods[x].changes[y].change_location + "</li>";} else if (ntMods[x].changes[y].change_type == "chirality") { chgtxt += "<li>" + ntMods[x].changes[y].parent_atom + "(" + ntMods[x].changes[y].parent_chirality + ")" + "<=>" + ntMods[x].changes[y].modified_atom + "(" + ntMods[x].changes[y].modified_chirality + ")|" + ntMods[x].changes[y].change_type + "|" + ntMods[x].changes[y].change_location + "</li>";} } } if (chgtxt == "") {chgtxt += "<li>no changes listed</li>";} chgtxt += "</ul>" text += "<td>" + ntMods[x].atom_count + "</td>"; if (detailstoggle == 1) {text += "<td>" + chgtxt + "</td>";} text += "<td>" + "<a href='/nakblist=nonstandard:" + x + "' target='_blank'>" + ntMods[x].count + "</a></td>"; text += "</tr>"; } //end for loop for ntMods text += "</tbody></table>"; document.getElementById("sourcetable").innerHTML = text; $('#sort').DataTable( { "lengthMenu": [[1, 10, 50, -1], [1, 10, 50, "All"]] , "oLanguage": { "sSearch": "Filter Table:" }, "columnDefs": [{"orderData": [1, 0], "targets": 1}, {"orderData": 0, "targets": 0}], "oSearch": { "sSearch": searchvar } } ); } //end getjson.onload getjson.open("GET", "https://rna.bgsu.edu/modified/modified_to_change_data.json", true); //getjson.open("GET", "js/modified_to_change_data.json", true); //local copy, may not be up to date getjson.send(); } //end on_select </script> <script> var elementhref = location.href.split("?"); function reset() { location.href = elementhref[0]; } </script> </html>

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