þÿ<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns="http://www.w3.org/TR/REC-html40"> <head> <meta http-equiv=Content-Type content="text/html; charset=unicodeFFFE"> <meta name=ProgId content=Word.Document> <meta name=Generator content="Microsoft Word 11"> <meta name=Originator content="Microsoft Word 11"> <link rel=File-List href="homology_modeling_files/filelist.xml"> <link rel=Edit-Time-Data href="homology_modeling_files/editdata.mso"> <!--[if !mso]> <style> v\:* {behavior:url(#default#VML);} o\:* {behavior:url(#default#VML);} w\:* {behavior:url(#default#VML);} .shape {behavior:url(#default#VML);} </style> <![endif]--><!--[if gte mso 9]><xml> <w:WordDocument> <w:FormsDesign/> <w:HyphenationZone>21</w:HyphenationZone> <w:ValidateAgainstSchemas/> <w:SaveIfXMLInvalid>false</w:SaveIfXMLInvalid> <w:IgnoreMixedContent>false</w:IgnoreMixedContent> <w:AlwaysShowPlaceholderText>false</w:AlwaysShowPlaceholderText> <w:BrowserLevel>MicrosoftInternetExplorer4</w:BrowserLevel> </w:WordDocument> </xml><![endif]--><!--[if gte mso 9]><xml> <w:LatentStyles DefLockedState="false" LatentStyleCount="156"> </w:LatentStyles> </xml><![endif]--> <style> <!-- /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {mso-style-parent:""; 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<o:p></o:p></span></p> <p class=MsoNormal><br> There are 5 questions (Q1-Q5) in this exercise that you need to answer. The people that are physically present can hand in a form that you will be given at the start of the exercise. <br> The &quot;online-students&quot; must email the answers to tnp@cbs.dtu.dk and write the PhD number in the subject field. Question Q2) is optional for the &quot;online-students&quot;. </p> <div class=MsoNormal align=center style='text-align:center'> <hr size=2 width="100%" align=center> </div> </div> <p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><br> The purpose of this exercise is to build 3D-models from protein sequences by use of homology modeling. Normally you want to see the 3D-structure of a protein that is of interest to you. A predicted model of a protein sequence might guide or just help you to interpret or plan experiments in the lab.<br> <br> 1) Are the terminal ends burried/exposed - Attatch a His-tag ?<br> 2) What residues define the active site ?<br> 3) Can I use the model to design a small molecule drug ?<br> 4) Can mutagenisis inactivate/optimize the function of the protein<br> <br> Several programs are avaliable but here three different modeling programs will be used. Secondly, the quality of the 3D-models are analyzed and finally a comparison can be made to the true protein structures. The two sequences below resemble an easy and a difficult homology modeling task. <br> The first protein is dihydroorotate dehydrogenase from common rat. This protein is involved in the pyrimidine biosynthesis, ubiquous in all organisms.<br> The second enzyme is employed by microorganisms during plant degradation (or &quot;soft-rot&quot;). <br> There were no experimental 3D structure at the time when the sequences were submitted to the three modeling-servers below. By now however the rat 3D structures is known as <a href="http://www.rcsb.org/pdb/navbarsearch.do?newSearch=yes&amp;isAuthorSearch=no&amp;radioset=All&amp;inputQuickSearch=1UUM&amp;image.x=0&amp;image.y=0&amp;image=Search">1UUM</a> where as the pectate lyase has not yet been submitted to the <a href="http://www.rcsb.org/pdb/Welcome.do">PDB</a> and it therefore still remains as a difficult target. &nbsp;<U7:P></U7:P><U6:P></U6:P> <o:p></o:p></span></p> <p><span lang=EN-US style='font-family:"Courier New";color:black;mso-ansi-language: EN-US'>&gt;RAT Dihydroorotate dehydrogenase [Rattus norvegicus]</span><span lang=EN-US style='mso-ansi-language:EN-US'> <br> </span><span lang=EN-US style='font-family:"Courier New";color:#009900; mso-ansi-language:EN-US'>MAWRQLRKRALDAVIILGGGGLLFTSYLTATGDDHFYAEYLMPGLQRLLDPESAHRLAVR</span><span lang=EN-US style='mso-ansi-language:EN-US'> <br> </span><span lang=EN-US style='font-family:"Courier New";color:#009900; mso-ansi-language:EN-US'>VTSLGLLPRATFQDSDMLEVKVLGHKFRNPVGIAAGFDKNGEAVDGLYKLGFGFVEVGSV</span><span lang=EN-US style='mso-ansi-language:EN-US'> <br> </span><span lang=EN-US style='font-family:"Courier New";color:#009900; mso-ansi-language:EN-US'>TPQPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAQLTADGLPLGIN</span><span lang=EN-US style='mso-ansi-language:EN-US'> <br> </span><span lang=EN-US style='font-family:"Courier New";color:#009900; mso-ansi-language:EN-US'>LGKNKTSEDAAADYAEGVRTLGPLADYLVVNVSSPNTAGLRSLQGKTELRHLLSKVLQER</span><span lang=EN-US style='mso-ansi-language:EN-US'> <br> </span><span lang=EN-US style='font-family:"Courier New";color:#009900; mso-ansi-language:EN-US'>DALKGTRKPAVLVKIAPDLTAQDKEDIASVARELGIDGLIVTNTTVSRPVGLQGALRSET</span><span lang=EN-US style='mso-ansi-language:EN-US'> <br> </span><span lang=EN-US style='font-family:"Courier New";color:#009900; mso-ansi-language:EN-US'>GGLSGKPLRDLSTQTIREMYALTQGRIPIIGVGGVSSGQDALEKIQAGASLVQLYTALIF</span><span lang=EN-US style='mso-ansi-language:EN-US'> <br> </span><span lang=EN-US style='font-family:"Courier New";color:#009900; mso-ansi-language:EN-US'>LGPPVVVRVKRELEALLKERGFTTVTDAIGADHRR<U7:P></U7:P></span><span lang=EN-US style='mso-ansi-language:EN-US'><U6:P></U6:P> <o:p></o:p></span></p> <p><span lang=EN-US style='font-family:"Courier New";color:black;mso-ansi-language: EN-US'>&gt;PE Pectate lyase [Thermotoga maritima]</span><span lang=EN-US style='mso-ansi-language:EN-US'> <br> </span><span lang=EN-US style='font-family:"Courier New";color:#009900; mso-ansi-language:EN-US'>SLNDKPVGFASVPTADLPEGTVGGLGGEIVFVRTAEELEKYTTAEGKYVIVVDGTIVFEP <br> KREIKVLSDKTIVGINDAKIVGGGLVIKDAQNVIIRNIHFEGFYMEDDPRGKKYDFDYIN <br> VENSHHIWIDHCTFVNGNDGAVDIKKYSNYITVSWCKFVDHDKVSLVGSSDKEDPEQAGQ <br> AYKVTYHHNYFKNCIQRMPRIRFGMAHVFNNFYSMGLRTGVSGNVFPIYGVASAMGAKVH <br> VEGNYFMGYGAVMAEAGIAFLPTRIMGPVEGYLTLGEGDAKNEFYYCKEPEVRPVEEGKP <br> ALDPREYYDYTLDPVQDVPKIVVDGAGAGKLVFEELNTAQ</span><span lang=EN-US style='mso-ansi-language:EN-US'> <br style='mso-special-character:line-break'> <![if !supportLineBreakNewLine]><br style='mso-special-character:line-break'> <![endif]><o:p></o:p></span></p> <p><b><u><span lang=EN-US style='color:black;mso-ansi-language:EN-US'><U7:P></U7:P><U6:P></U6:P>The concept of modeling is</span></u></b><u><span lang=EN-US style='color:black; mso-ansi-language:EN-US'>:<U7:P></U7:P></span></u><span lang=EN-US style='mso-ansi-language:EN-US'><U6:P></U6:P> <o:p></o:p></span></p> <p><span lang=EN-US style='color:black;mso-ansi-language:EN-US'>1) Find one or more suitable template(s) with known structures</span><span lang=EN-US style='mso-ansi-language:EN-US'> <br> <span style='color:black'>2) Align the query sequence of interest with the templates</span> <br> <span style='color:black'>3) Thread the query sequence onto the template structure</span> <br> <span style='color:black'>4) Energy minimisation<U7:P></U7:P></span><U6:P></U6:P> <o:p></o:p></span></p> <div class=MsoNormal align=center style='text-align:center'> <hr size=2 width="100%" align=center> </div> <div style='mso-element:frame;mso-element-wrap:around;mso-height-rule:exactly'> <table cellspacing=0 cellpadding=0 hspace=0 vspace=0 align=left> <tr> <td valign=top align=left style='padding-top:0cm;padding-right:7.05pt; padding-bottom:0cm;padding-left:7.05pt'> <h2><span lang=EN-US>Initial Questions</span></h2> </td> </tr> </table> </div> <p class=MsoNormal align=center style='text-align:center'><o:p>&nbsp;</o:p></p> <p class=MsoNormal>Q1) What are the names of the four backbone atoms in a protein ?<br> Q2) Draw a di-peptide and indicate the sidechain with &quot;R&quot; </p> <div class=MsoNormal align=center style='text-align:center'> <hr size=2 width="100%" align=center> </div> <p class=MsoNormal align=center style='text-align:center'><b><span lang=EN-US style='font-size:18.0pt;mso-ansi-language:EN-US'>Validating your alignment and submitting a modeling request<U7:P></U7:P></span></b><span lang=EN-US style='mso-ansi-language:EN-US'><U6:P></U6:P><o:p></o:p></span></p> <p><U7:P></U7:P><span lang=EN-US style='mso-ansi-language:EN-US'>The two query sequences have been submittet to three homology modeling servers and the resulting pdb models are linked below. Pressing the link to the <b>pdb.file</b> enables you to see the 3D-structure, whereas the <b>file.txt</b> contains the text output from the modeling server. You may (optional) submit the PE-sequence to the local modeling server <a href="http://www.cbs.dtu.dk/services/CPHmodels-2.0">CPHmodels</a>. This will take approx. 3 minutes.<br> Fill in the empty fields below. <br> <br> Alignment technology in short utilized by CPHmodels: <br> Query sequence is blasted against the PDB database. If a PDB hit is found then <b>a)</b> else <b>b)</b><br> <b>a)</b> Align Query sequence and PDB sequence by use of a Blosum62 matrix. <br> <b>b)</b> Query sequence is blasted against SwissProt/nr database and a sequence profile is generated. Now search the PDB database with the query sequence profile. If still no PDB hit is found then search one more iteration agains SwissProt (Continue 3-4 iterations). If a PDB hit is found then make a sequence profile and align the query and target sequences by use of a profile-profile alignment. <br> &nbsp; <br> NB ! A residue is an amino acid. &nbsp; <br> &nbsp; <o:p></o:p></span></p> <form> <table class=MsoNormalTable border=1 cellpadding=0 width="75%" style='width:75.0%;mso-cellspacing:1.5pt;mso-padding-alt:0cm 0cm 0cm 0cm'> <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><b><span lang=EN-US style='mso-ansi-language:EN-US'>Modeling servers<o:p></o:p></span></b></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><b><span lang=EN-US style='mso-ansi-language:EN-US'>rat models<o:p></o:p></span></b></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><b><span lang=EN-US style='mso-ansi-language:EN-US'>Residues in model<o:p></o:p></span></b></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><b><span lang=EN-US style='mso-ansi-language:EN-US'>pe models<o:p></o:p></span></b></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><b><span lang=EN-US style='mso-ansi-language:EN-US'>Residues in model<o:p></o:p></span></b></p> </td> </tr> <tr style='mso-yfti-irow:1'> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><a href="http://www.expasy.ch/swissmod/SM_FIRST.html">SwissModel</a></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/rat_1.pdb">rat_1.pdb</a></p> <p><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/rat_1.txt">rat_1.txt</a></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="5"></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/pe_1.pdb">pe_1.pdb</a></p> <p><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/pe_1.txt">pe_1.txt</a></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="5"></p> </td> </tr> <tr style='mso-yfti-irow:2'> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><a href="http://www.bmm.icnet.uk/servers/3djigsaw/">3Djigsaw</a></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/rat_2.pdb">rat_2.pdb</a></p> <p><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/rat_2.txt">rat_2.txt</a></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="5"></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/pe_2.pdb">pe_2.pdb</a></p> <p><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/pe_2.txt">pe_2.txt</a></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="5"></p> </td> </tr> <tr style='mso-yfti-irow:3;mso-yfti-lastrow:yes'> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><a href="http://www.cbs.dtu.dk/services/CPHmodels-2.0">CPHmodels</a></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/rat_3.pdb">rat_3.pdb</a></p> <p><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/rat_3.txt">rat_3.txt</a></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="5"></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/pe_3.pdb">pe_3.pdb</a></p> <p><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/pe_3.txt">pe_3.txt</a></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="5"></p> </td> </tr> </table> </form> <p>The output from homology modeling servers vary much eg the information about target sequence used, sequence alignment and number of residues in the model. In fact four residues (60, 104-106) are missing in the pe_2 model produced by the 3Djigsaw.<br> <br> The homology modeling servers have chosen different templates to make the 'pe-models'. SwissModel used 1QCX:A and CPHmodels used 1BN8:A. This is due to different search algorithms used by the two programs. To explore how similar the templates are the CE-alignment program can be used to verify sequence/structure similarities, based on a structural super-positioning.<br> Compare the structure of two templates by use of the structural alignment program CE.<br> After having aligned the two sequences within the CE-program, do this: <b>&quot;Press to start Compare3D&quot;</b>. </p> <table class=MsoNormalTable border=1 cellpadding=0 width="75%" style='width:75.0%;mso-cellspacing:1.5pt;mso-padding-alt:0cm 0cm 0cm 0cm'> <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes;mso-yfti-lastrow:yes'> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><a href="http://cl.sdsc.edu/ce/ce_align.html">CE server</a><o:p></o:p></span></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'>Template SwissModel 1QCX:A<o:p></o:p></span></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'>Template CPHmodels 1BN8:A<o:p></o:p></span></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'>Rmsd<INPUT TYPE="TEXT" SIZE="5"></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'>% id<INPUT TYPE="TEXT" SIZE="5"></p> </td> </tr> </table> <p><span style='color:red'><U7:P></U7:P><U7:P></U7:P><U6:P></U6:P>&nbsp;<o:p></o:p></span></p> <p><b><span lang=EN-US style='color:red;mso-ansi-language:EN-US'>Checking Model quality:</span></b><span lang=EN-US style='color:red;mso-ansi-language:EN-US'><br> </span><span lang=EN-US style='mso-ansi-language:EN-US'><U7:P></U7:P>A handy tool for locating areas causing trouble is the &quot;Ramachandran Plot&quot;. A Ramachandran plot visualises the torsion angles of the peptide backbone and almost all residues of natural proteins are found within the areas denoted on the plot. An exception is glycine and proline residues. Problems with the peptide backbone are quickly spotted with this tool as seen in <a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/1rip_01.pdf">&quot;A bad Ramachandran plot&quot;</a>.<br> <a href="http://www.expasy.ch/swissmod/SM_ModelAccuracy.html">Click here for more information on accuracy determination.</a> A good model has &gt; 90% of the residues in core region of a Rahachandran plot and &gt;98% in the core+allowed region.<br> Q3) Which atoms define the phi and psi dihedral angles ? (Search the internet).<U7:P></U7:P><U6:P></U6:P> <o:p></o:p></span></p> <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b><span lang=EN-US style='color:red;mso-ansi-language:EN-US'><U7:P></U7:P><U6:P></U6:P>Ramachandran plot</span></b><span lang=EN-US style='color:red;mso-ansi-language:EN-US'>:<U7:P></U7:P></span><span lang=EN-US style='mso-ansi-language:EN-US'><U6:P></U6:P> <br> &nbsp; <o:p></o:p></span></p> <table class=MsoNormalTable border=1 cellpadding=0 width="75%" style='width:75.0%;mso-cellspacing:1.5pt;mso-padding-alt:0cm 0cm 0cm 0cm' cols=4 NOSAVE> <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><b><span lang=EN-US style='mso-ansi-language:EN-US'>Ramachandran summary file</span></b><span lang=EN-US style='mso-ansi-language:EN-US'><o:p></o:p></span></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><b><span lang=EN-US style='mso-ansi-language:EN-US'>Ramachandran plot<U6:P></U6:P></span></b><span lang=EN-US style='mso-ansi-language:EN-US'><o:p></o:p></span></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><b><span lang=EN-US style='mso-ansi-language:EN-US'>Core+allowed (%)<U6:P></U6:P></span></b><span lang=EN-US style='mso-ansi-language:EN-US'><o:p></o:p></span></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><b><span lang=EN-US style='mso-ansi-language:EN-US'>Disallowed (%)<U6:P></U6:P></span></b><span lang=EN-US style='mso-ansi-language:EN-US'><o:p></o:p></span></p> </td> </tr> <tr style='mso-yfti-irow:1'> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><U6:P></U6:P><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/rat_1_sum.txt">rat_1</a><U6:P></U6:P><o:p></o:p></span></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/rat_1_rama.pdf">rat_1_rama.pdf</a><U6:P></U6:P><o:p></o:p></span></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="4"></p> <p class=MsoNormal>&nbsp; </p> </td> <U6:P></U6:P> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="4"></p> </td> </tr> <U6:P></U6:P> <tr style='mso-yfti-irow:2'> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><U6:P></U6:P><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/rat_2_sum.txt">rat_2</a><U6:P></U6:P></span></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/rat_2_rama.pdf">rat_2_rama.pdf</a><U6:P></U6:P></span></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="4"></p> </td> <U6:P></U6:P> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="4"></p> </td> </tr> <U6:P></U6:P> <tr style='mso-yfti-irow:3'> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><U6:P></U6:P><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/rat_3_sum.txt">rat_3</a><U6:P></U6:P></span></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/rat_3_rama.pdf">rat_3_rama.pdf</a><U6:P></U6:P></span></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="4"></p> </td> <U6:P></U6:P> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="4"></p> </td> </tr> <U6:P></U6:P> <tr style='mso-yfti-irow:4'> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><U6:P></U6:P><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/pe_1_sum.txt">pe_1</a><U6:P></U6:P></span></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/pe_1_rama.pdf">pe_1_rama.pdf</a><U6:P></U6:P></span></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="4"></p> </td> <U6:P></U6:P> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="4"></p> </td> </tr> <U6:P></U6:P> <tr style='mso-yfti-irow:5'> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><U6:P></U6:P><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/pe_2_sum.txt">pe_2</a><U6:P></U6:P></span></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/pe_2_rama.pdf">pe_2_rama.pdf</a><U6:P></U6:P></span></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="4"></p> </td> <U6:P></U6:P> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="4"></p> </td> </tr> <U6:P></U6:P> <tr style='mso-yfti-irow:6;mso-yfti-lastrow:yes'> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><U6:P></U6:P><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/pe_3_sum.txt">pe_3</a><U6:P></U6:P></span></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/pe_3_rama.pdf">pe_3_rama.pdf</a><U6:P></U6:P></span></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="4"></p> </td> <U6:P></U6:P> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="4"></p> </td> </tr> <U6:P></U6:P> </table> <div class=MsoNormal align=center style='text-align:center'> <hr size=2 width="100%" align=center> </div> <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=EN-US style='mso-ansi-language:EN-US'>To get a more quantitative measure for the alignments, you can calculate the root mean square deviation (rmsd) between the true structure (chain 1) and the model (chain 2) by use of the CE server. The output from the CE-server is shown below. The term 'alignment length' is used as a measure of how many residues that have been aligned to another residue eg. alignment to gaps are excluded.Therefore be aware that %id and %gaps do not need to add up to 100%.<U7:P></U7:P><U6:P></U6:P> <o:p></o:p></span></p> <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b><span lang=EN-US style='color:red;mso-ansi-language:EN-US'><U6:P></U6:P>Correctness of the models:<U7:P></U7:P></span></b><span lang=EN-US style='mso-ansi-language: EN-US'><U6:P></U6:P> <br> &nbsp; <o:p></o:p></span></p> <table class=MsoNormalTable border=1 cellpadding=0 width="75%" style='width:75.0%;mso-cellspacing:1.5pt;mso-padding-alt:0cm 0cm 0cm 0cm' cols=3 NOSAVE> <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><b><span lang=EN-US style='mso-ansi-language:EN-US'>Ce alignment</span></b><span lang=EN-US style='mso-ansi-language:EN-US'><o:p></o:p></span></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <h3><span lang=EN-US>Ce align length</span></h3> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><b><span lang=EN-US style='mso-ansi-language:EN-US'>CE rmsd (Å)<U6:P></U6:P></span></b><span lang=EN-US style='mso-ansi-language:EN-US'><o:p></o:p></span></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><b><span lang=EN-US style='mso-ansi-language:EN-US'>% id<U6:P></U6:P></span></b><span lang=EN-US style='mso-ansi-language:EN-US'><o:p></o:p></span></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><b><span lang=EN-US style='mso-ansi-language:EN-US'># of correct residues in model<U6:P></U6:P></span></b><span lang=EN-US style='mso-ansi-language:EN-US'><o:p></o:p></span></p> </td> </tr> <tr style='mso-yfti-irow:1'> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/rat_1_ce.txt">rat_1</a><U6:P></U6:P></span></p> </td> <U6:P></U6:P> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'>171<o:p></o:p></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><U6:P></U6:P>0.84</p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="4"></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="4"></p> </td> </tr> <tr style='mso-yfti-irow:2'> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/rat_2_ce.txt">rat_2</a><U6:P></U6:P></span></p> </td> <U6:P></U6:P> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'>169<o:p></o:p></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><U6:P></U6:P>1.25</p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="4"></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="4"></p> </td> </tr> <tr style='mso-yfti-irow:3'> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/rat_3_ce.txt">rat_3<U6:P></U6:P></a></span><span class=MsoHyperlink><o:p></o:p></span></p> <p class=MsoNormal><o:p>&nbsp;</o:p></p> </td> <U6:P></U6:P> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'>171<o:p></o:p></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><U6:P></U6:P>0.81</p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="4"></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="4"></p> </td> </tr> <tr style='mso-yfti-irow:4'> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/pe_1_ce.txt"><span lang=DA style='mso-ansi-language:DA'>pe_1</span></a><U6:P></U6:P></span></p> </td> <U6:P></U6:P> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'>48<o:p></o:p></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><U6:P></U6:P>1.17</p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="4"></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="4"></p> </td> </tr> <tr style='mso-yfti-irow:5'> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/pe_2_ce.txt"><span lang=DA style='mso-ansi-language:DA'>pe_2</span></a><U6:P></U6:P></span></p> </td> <U6:P></U6:P> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'>186<o:p></o:p></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><U6:P></U6:P>2.86</p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="4"></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="4"></p> </td> </tr> <tr style='mso-yfti-irow:6;mso-yfti-lastrow:yes'> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><span lang=EN-US style='mso-ansi-language:EN-US'><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/pe_3_ce.txt"><span lang=DA style='mso-ansi-language:DA'>pe_3</span></a><U6:P></U6:P></span></p> </td> <U6:P></U6:P> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'>168<o:p></o:p></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><U6:P></U6:P>1.85</p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="4"></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="4"></p> </td> </tr> </table> <p class=MsoNormal><U7:P></U7:P>&nbsp;<o:p></o:p></p> <U7:P></U7:P><U6:P></U6:P><U7:P></U7:P> <div class=MsoNormal align=center style='text-align:center'> <hr size=2 width="100%" align=center> </div> <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b><span lang=EN-US style='color:red;mso-ansi-language:EN-US'><U6:P></U6:P>Predicting model quality by use of ProQ:<U7:P></U7:P></span></b><span lang=EN-US style='mso-ansi-language:EN-US'><U6:P></U6:P> &nbsp; <o:p></o:p></span></p> <p class=MsoNormal><br> <br> The paper describing the ProQ method can be seen here: <a href="http://www.sbc.su.se/~bjornw/papers/correct_models.pdf">&quot;<i>Can correct models be identified</i>&quot;</a> <br> Use the <a href="http://www.sbc.su.se/~bjornw/ProQ/ProQ.cgi">ProQ predictor</a> to verify the correctness of the six models. </p> <form> <table class=MsoNormalTable border=1 cellpadding=0 width="75%" style='width:75.0%;mso-cellspacing:1.5pt;mso-padding-alt:0cm 0cm 0cm 0cm'> <tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><b><span lang=EN-US style='mso-ansi-language:EN-US'>Modeling server<o:p></o:p></span></b></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><b><span lang=EN-US style='mso-ansi-language:EN-US'>rat models<o:p></o:p></span></b></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><b><span lang=EN-US style='mso-ansi-language:EN-US'>LGscore<o:p></o:p></span></b></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal><b><span lang=EN-US style='mso-ansi-language:EN-US'>pe models<o:p></o:p></span></b></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><b><span lang=EN-US style='mso-ansi-language:EN-US'>LGscore<o:p></o:p></span></b></p> </td> </tr> <tr style='mso-yfti-irow:1'> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal>SwissModel</p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/rat_1.txt">rat_1.txt</a></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="5"></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/pe_1.txt">pe_1.txt</a></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="5"></p> </td> </tr> <tr style='mso-yfti-irow:2'> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal>3Djigsaw</p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/rat_2.txt">rat_2.txt</a></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="5"></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/pe_2.txt">pe_2.txt</a></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="5"></p> </td> </tr> <tr style='mso-yfti-irow:3;mso-yfti-lastrow:yes'> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal>CPHmodels</p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/rat_3.txt">rat_3.txt</a></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="5"></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p><a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/lund/homology/pe_3.txt">pe_3.txt</a></p> </td> <td style='padding:.75pt .75pt .75pt .75pt'> <p class=MsoNormal align=center style='text-align:center'><INPUT TYPE="TEXT" SIZE="5"></p> </td> </tr> </table> </form> <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b><span lang=EN-US style='color:red;mso-ansi-language:EN-US'><U6:P></U6:P>Ranking the modeling servers 1 - 3, where 1 is best:<U7:P></U7:P></span></b><span lang=EN-US style='mso-ansi-language:EN-US'><U6:P></U6:P> &nbsp; <o:p></o:p></span></p> <p class=MsoNormal style='margin-bottom:12.0pt'>Q4) Which of the modeling server(s) made the most reliable rat/pe models based on the Ramachandran analysis and the ProQ predictions ? <br> Q5) In the &quot;correctness of models&quot; the true 3D-structures of &quot;rat&quot; and &quot;pe&quot; were known. What is the ranking of the modeling-servers based on that analysis. <o:p></o:p></p> <p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b><span lang=EN-US style='color:red;mso-ansi-language:EN-US'><U6:P></U6:P>Key points:<U7:P></U7:P></span></b><span lang=EN-US style='mso-ansi-language:EN-US'><U6:P></U6:P> &nbsp; <o:p></o:p></span></p> <p class=MsoNormal>It is often possible to build a model by use of a modeling-server. The fact that a model can be built is no guarantee that it is correct. Try out several modeling-servers and chose the model that seems best with respect to Ramachandran quality and ProQ scores. The sequence alignment is the most critical step in the modeling process. </p> </div> </body> </html>