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<p class="MsoNormal" style="margin-bottom:12.0pt"><span lang="EN-US"><br>
</span><b><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif"">NBIC PhD course Protein Structures: production, prowess, power, promises, and problems
</span></b><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif""><br>
<br>
<br>
<u>Date:</u> </span><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif";color:#1F497D">4 – 8 Nov 2013</span><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif"">
<br>
<u>Course coordinator</u>: Gert Vriend</span><span lang="EN-US"><br>
</span><u><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif"">Location:</span></u><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif""> Center for Molecular and Biomolecular
Informatics (CMBI), UMC Radboud, Nijmegen, the Netherlands<br>
<u>Website: </u><a href="http://www.nbic.nl/education/nbic-phd-school/course-schedule/protein-structures-production-prowess-power-promises-and-problems/">http://www.nbic.nl/education/nbic-phd-school/course-schedule/protein-structures-production-prowess-power-promises-and-problems/</a>
<u> </u><br>
<u>Registration:</u> <a href="http://www.nbic.nl/education/nbic-phd-school/enrolment/">
http://www.nbic.nl/education/nbic-phd-school/enrolment/</a></span><span lang="EN-US"><br>
<br>
<o:p></o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif"">Target audience</span></b><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif"">The course is suitable for both PhD students working in structural bioinformatics as well as for PhD students
in the life sciences who want to learn more about using structural informatioin in their research.
<br>
The course schedule accommodates both groups, parallel sessions for both groups will be scheduled when necessary.</span><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Trebuchet MS","sans-serif"">
</span><o:p></o:p></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif"">Course Description
</span></b><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif"">In the right hands, protein structures are a 'power'ful tool to answer bio-molecular questions. Knowledge of
the structure is a pre-requisite for rational drug design, for biotechnology, for chemical biology, and for answering a whole series of biomedical questions. In this course we will discuss the 'production' of protein structures by NMR, X-ray, and homology
modelling. These methods all have their pro's and cons so a certain 'prowess' is needed to follow all 'promises' and start attacking bio-medical 'problems' using protein structures.</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif"">The course will be split in three parts.</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif"">Part 1) Looking and seeing things in protein structures, learning to operate the software, understanding some of the algorithms.</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif"">Part 2) Protein structure determination (prediction) with NMR, X-ray, and homology modelling, and the possibilities and problems that come
with each of these three techniques.</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif"">Part 3) Applying all that was learned in real-life example studies.</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif""><br>
<b>Course topics<br>
</b><br>
Day 1: Homology modelling <br>
Day 2: Protein structure determination and validation </span><span lang="EN-US"><br>
</span><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif"">Day 3: Electrostatics and molecular dynamics
</span><span lang="EN-US"><br>
</span><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif"">Day 4: Protein structure comparison
<br>
Day 5: Own project executed with help from CMBI staff.</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif""><br>
Examples of questions you will be able to answer after foll</span><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif";color:#1F497D">o</span><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif"">wing
the course:</span><span lang="EN-US" style="font-size:11.0pt;line-height:115%;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<![if !supportLists]><span lang="EN-US" style="font-family:Symbol"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">Why is a person with this mutation sick? Or in other words, how does the molecular phenotype cause a disease state?</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoListParagraph" style="margin-left:54.0pt;text-indent:-18.0pt;mso-list:l0 level1 lfo2">
<![if !supportLists]><span lang="EN-US" style="font-family:Symbol"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">This enzyme converts mannose. Can I make is specificity broader?</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoListParagraph" style="margin-left:54.0pt;text-indent:-18.0pt;mso-list:l0 level1 lfo2">
<![if !supportLists]><span lang="EN-US" style="font-family:Symbol"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">This enzyme doesn't function in my in vitro assay. Should I add some ions?</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoListParagraph" style="margin-left:54.0pt;text-indent:-18.0pt;mso-list:l0 level1 lfo2">
<![if !supportLists]><span lang="EN-US" style="font-family:Symbol"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">I want to add a tag to my enzyme, should I put it on the N-terminus, the C-terminus, or is something different needed?</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoListParagraph" style="margin-left:54.0pt;text-indent:-18.0pt;mso-list:l0 level1 lfo2">
<![if !supportLists]><span lang="EN-US" style="font-family:Symbol"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">This receptor binds a ligand, but if I look at the structure, that ligand doesn't fit at all. Can I predict motions that take place upon ligand binding?</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif";color:#1F497D"><o:p> </o:p></span></b></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;line-height:115%;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></b></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif"">NBIC PhD School</span></b><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif"">This course is part of the Education Programme of the NBIC PhD School. The NBIC PhD School offers training and education for PhD students
in bioinformatics. <br>
More information about the NBIC PhD School can also be found on <a href="http://www.nbic.nl">
http://www.nbic.nl</a> => Education => NBIC PhD School. </span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif""> </span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif"">More information</span></b><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif"">For more information about the course you can contact Celia van Gelder (NBIC Education) at
<a href="mailto:celia.van.gelder@nbic.nl">celia.van.gelder@nbic.nl</a>. <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;line-height:115%;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;line-height:115%;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal">-- <span style="font-size:11.0pt;line-height:115%;font-family:"Calibri","sans-serif";color:#1F497D">
<o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:normal"><span style="font-size:10.5pt;font-family:Consolas;color:#1F497D">Dr. Celia W.G. van Gelder<o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:normal"><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas;color:#1F497D">Coordinator Education CMBI<o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:normal"><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas;color:#1F497D">Projectleader Education NBIC<o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:normal"><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas;color:#1F497D">tel. +31-(0)24-3666120<o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:normal"><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas;color:#1F497D">e-mail:
</span><a href="mailto:C.vanGelder@umcn.nl"><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas;color:blue">C.vanGelder@umcn.nl</span></a><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas;color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:normal"><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas;color:#1F497D">websites:
</span><a href="http://www.cmbi.ru.nl"><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas;color:blue">www.cmbi.ru.nl</span></a><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas;color:#1F497D">,
</span><a href="http://www.nbic.nl"><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas;color:blue">www.nbic.nl</span></a><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas;color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:normal"><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal" style="line-height:normal"><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas;color:#1F497D">Postal address:<o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:normal"><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas;color:#1F497D">CMBI 260<o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:normal"><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas;color:#1F497D">Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands<o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:normal"><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;line-height:115%;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt;line-height:normal"><span lang="EN-US"><o:p> </o:p></span></p>
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Het UMC St Radboud staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629.<BR> The Radboud University Nijmegen Medical Centre is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.<BR>
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