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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif";color:windowtext">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";color:windowtext"><br>
<br>
<br>
<u>Date:</u> 4 – 8 Nov 2013 <br>
<u>Course coordinator</u>: Gert Vriend</span><span lang="EN-US" style="color:windowtext"><br>
</span><u><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif";color:windowtext">Location:</span></u><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif";color:windowtext">
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/" target="_blank"><span style="color:windowtext">http://www.nbic.nl/education/nbic-phd-school/course-schedule/protein-structures-production-prowess-power-promises-and-problems/</span></a>
<u> <br>
Course website:</u> http://swift.cmbi.ru.nl/teach/AIOC/index.html<br>
<u>Registration:</u> <a href="http://www.nbic.nl/education/nbic-phd-school/enrolment/" target="_blank">
<span style="color:windowtext">http://www.nbic.nl/education/nbic-phd-school/enrolment/</span></a></span><span lang="EN-US" style="color:windowtext"><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:windowtext">Target audience</span></b><span style="color:windowtext"><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";color:windowtext">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";color:windowtext">
</span><span style="color:windowtext"><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:windowtext">Course Description
</span></b><span style="color:windowtext"><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";color:windowtext">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 style="color:windowtext"><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";color:windowtext">The course will be split in three parts.</span><span style="color:windowtext"><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";color:windowtext">Part 1) Looking and seeing things in protein structures, learning to operate the software, understanding some of the algorithms.</span><span style="color:windowtext"><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";color:windowtext">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 style="color:windowtext"><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";color:windowtext">Part 3) Applying all that was learned in real-life example studies.</span><span style="color:windowtext"><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";color:windowtext"><br>
<b>Course topics<br>
</b><br>
Day 1: Homology modelling <br>
Day 2: Protein structure determination and validation </span><span lang="EN-US" style="color:windowtext"><br>
</span><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif";color:windowtext">Day 3: Electrostatics and molecular dynamics
</span><span lang="EN-US" style="color:windowtext"><br>
</span><span lang="EN-US" style="font-size:10.0pt;line-height:115%;font-family:"Helvetica","sans-serif";color:windowtext">Day 4: Protein structure comparison
<br>
Day 5: Own project executed with help from CMBI staff.</span><span style="color:windowtext"><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";color:windowtext"><br>
Examples of questions you will be able to answer after following the course:</span><span style="color:windowtext"><o:p></o:p></span></p>
<p class="MsoListParagraph" style="margin-left:54.0pt;text-indent:-18.0pt"><span lang="EN-US" style="font-family:Symbol;color:windowtext">·</span><span lang="EN-US" style="font-size:7.0pt;color:windowtext">
</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:windowtext">Why is a person with this mutation sick? Or in other words, how does the molecular phenotype cause a disease state?</span><span style="color:windowtext"><o:p></o:p></span></p>
<p class="MsoListParagraph" style="margin-left:54.0pt;text-indent:-18.0pt"><span lang="EN-US" style="font-family:Symbol;color:windowtext">·</span><span lang="EN-US" style="font-size:7.0pt;color:windowtext">
</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:windowtext">This enzyme converts mannose. Can I make is specificity broader?</span><span style="color:windowtext"><o:p></o:p></span></p>
<p class="MsoListParagraph" style="margin-left:54.0pt;text-indent:-18.0pt"><span lang="EN-US" style="font-family:Symbol;color:windowtext">·</span><span lang="EN-US" style="font-size:7.0pt;color:windowtext">
</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:windowtext">This enzyme doesn't function in my in vitro assay. Should I add some ions?</span><span style="color:windowtext"><o:p></o:p></span></p>
<p class="MsoListParagraph" style="margin-left:54.0pt;text-indent:-18.0pt"><span lang="EN-US" style="font-family:Symbol;color:windowtext">·</span><span lang="EN-US" style="font-size:7.0pt;color:windowtext">
</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:windowtext">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 style="color:windowtext"><o:p></o:p></span></p>
<p class="MsoListParagraph" style="margin-left:54.0pt;text-indent:-18.0pt"><span lang="EN-US" style="font-family:Symbol;color:windowtext">·</span><span lang="EN-US" style="font-size:7.0pt;color:windowtext">
</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:windowtext">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 style="color:windowtext"><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:windowtext"> </span></b><span style="color:windowtext"><o:p></o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;line-height:115%;font-family:"Calibri","sans-serif";color:windowtext"> </span></b><span style="color:windowtext"><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:windowtext">NBIC PhD School</span></b><span style="color:windowtext"><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";color:windowtext">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" target="_blank">
<span style="color:windowtext">http://www.nbic.nl</span></a> => Education => NBIC PhD School.
</span><span style="color:windowtext"><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";color:windowtext"> </span><span style="color:windowtext"><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:windowtext">More information</span></b><span style="color:windowtext"><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";color:windowtext">For more information about the course you can contact Celia van Gelder (NBIC Education) at
<a href="mailto:celia.van.gelder@nbic.nl" target="_blank"><span style="color:windowtext">celia.van.gelder@nbic.nl</span></a>.
</span><span style="color:windowtext"><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:windowtext"> </span><span style="color:windowtext"><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:windowtext"> </span><span style="color:windowtext"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">-- <o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:normal"><span style="font-size:10.5pt;font-family:Consolas;color:windowtext">Dr. Celia W.G. van Gelder</span><span style="color:windowtext"><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:windowtext">Coordinator Education CMBI</span><span style="color:windowtext"><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:windowtext">Projectleader Education NBIC</span><span style="color:windowtext"><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:windowtext">tel. +31-(0)24-3666120</span><span style="color:windowtext"><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:windowtext">e-mail:
</span><span style="color:windowtext"><a href="mailto:C.vanGelder@umcn.nl" target="_blank"><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas;color:windowtext">C.vanGelder@umcn.nl</span></a><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:windowtext">websites:
</span><span style="color:windowtext"><a href="http://www.cmbi.ru.nl" target="_blank"><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas;color:windowtext">www.cmbi.ru.nl</span></a></span><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas;color:windowtext">,
</span><span style="color:windowtext"><a href="http://www.nbic.nl" target="_blank"><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas;color:windowtext">www.nbic.nl</span></a><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:windowtext"> </span><span style="color:windowtext"><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:windowtext">Postal address:</span><span style="color:windowtext"><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:windowtext">CMBI 260</span><span style="color:windowtext"><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:windowtext">Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands</span><span style="color:windowtext"><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:windowtext"> </span><span style="color:windowtext"><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:windowtext"> </span><span style="color:windowtext"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt;line-height:normal"><span lang="EN-US" style="color:windowtext"> </span><span style="color:windowtext"><o:p></o:p></span></p>
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