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<small><font face="Helvetica, Arial, sans-serif"><b>NBIC PhD course
Protein Structures: production, prowess, power, promises, and problems </b><br>
<br>
<br>
</font></small><small><font face="Helvetica, Arial, sans-serif"><u>Date:</u>
31 Oct- 4 Nov 2011 <br>
</font></small><small><font face="Helvetica, Arial, sans-serif"><u>Course
coordinator</u>: Gert Vriend</font></small><br>
<small><font face="Helvetica, Arial, sans-serif"> <u>Location:</u>
Center for Molecular and Biomolecular Informatics (CMBI), UMC Radboud,
Nijmegen, the Netherlands<br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://www.nbic.nl/education/nbic-phd-school/enrolment/"></a><u>Website:
</u><a class="moz-txt-link-freetext" 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>
</font></small><small><font face="Helvetica, Arial, sans-serif"><u>Registration:</u>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://www.nbic.nl/education/nbic-phd-school/enrolment/">http://www.nbic.nl/education/nbic-phd-school/enrolment/</a></font></small><br>
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<p class="MsoNormal" style=""><b style=""><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US">Target audience</span><i style=""><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US"><o:p></o:p></span></i></b></p>
<span style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US">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
style="font-size: 10pt; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US"><span style=""> <br>
<br>
</span></span>
<p class="MsoNormal" style=""><b style=""><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US">Course Description </span><i style=""><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US"><o:p></o:p></span></i></b></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US">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.<br>
<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US">The
course will be split in three parts.<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US">Part
1) Looking and seeing things in protein structures, learning to operate
the
software, understanding some of the algorithms.<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US">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.<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US">Part
3) Applying all that was learned in real-life example studies.<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US"><o:p><br>
<b>Course topics<br>
</b></o:p></span>
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<![endif]--><span
style="font-size: 10pt; line-height: 115%; font-family: "Helvetica","sans-serif";"
lang="EN-US"><br>
Day 1: Homology modelling <o:p></o:p></span><span
style="font-size: 10pt; line-height: 115%; font-family: "Helvetica","sans-serif";"
lang="EN-US"><br>
Day 2: Protein structure determination and validation <o:p></o:p></span><br>
<span
style="font-size: 10pt; line-height: 115%; font-family: "Helvetica","sans-serif";"
lang="EN-US">Day 3: Electrostatics and molecular dynamics <o:p></o:p></span><br>
<span
style="font-size: 10pt; line-height: 115%; font-family: "Helvetica","sans-serif";"
lang="EN-US">Day 4: Protein structure comparison <o:p></o:p></span><span
style="font-size: 10pt; line-height: 115%; font-family: "Helvetica","sans-serif";"
lang="EN-US"><br>
Day 5: Own project executed with
help from CMBI staff.</span><br>
</p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US"><br>
Examples
of questions you will be able to answer after follwing the course:<o:p></o:p></span></p>
<p class="MsoListParagraphCxSpFirst"
style="margin-left: 54pt; text-indent: -36pt;"><!--[if !supportLists]--><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US"><span style="">1)<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal; -x-system-font: none;">
</span></span></span><!--[endif]--><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US">Why is a person with this mutation sick?
Or in other words, how does the molecular phenotype cause a disease
state?<o:p></o:p></span></p>
<p class="MsoListParagraphCxSpMiddle"
style="margin-left: 54pt; text-indent: -36pt;"><!--[if !supportLists]--><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US"><span style="">2)<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal; -x-system-font: none;">
</span></span></span><!--[endif]--><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US">This enzyme converts mannose. Can I make
is specificity broader?<o:p></o:p></span></p>
<p class="MsoListParagraphCxSpMiddle"
style="margin-left: 54pt; text-indent: -36pt;"><!--[if !supportLists]--><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US"><span style="">3)<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal; -x-system-font: none;">
</span></span></span><!--[endif]--><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US">This enzyme doesn't function in my in
vitro assay. Should I add some ions?<o:p></o:p></span></p>
<p class="MsoListParagraphCxSpMiddle"
style="margin-left: 54pt; text-indent: -36pt;"><!--[if !supportLists]--><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US"><span style="">4)<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal; -x-system-font: none;">
</span></span></span><!--[endif]--><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US">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?<o:p></o:p></span></p>
<p class="MsoListParagraphCxSpLast"
style="margin-left: 54pt; text-indent: -36pt;"><!--[if !supportLists]--><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US"><span style="">5)<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal; -x-system-font: none;">
</span></span></span><!--[endif]--><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US">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?<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US">More
information about the course programme can be found on:<i style=""> <br>
</i><a class="moz-txt-link-freetext" 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>.</span><i
style=""><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US"><o:p> </o:p></span></i><br>
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<p class="MsoNormal" style=""><b style=""><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US">NBIC PhD School</span><i style=""><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US"><o:p></o:p></span></i></b></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US">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 class="moz-txt-link-freetext" href="http://www.nbic.nl">http://www.nbic.nl</a> =>
Education => NBIC PhD School.<span style=""> </span><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US"><span style=""> </span><o:p></o:p></span></p>
<p class="MsoNormal" style=""><b style=""><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US">More information</span><i style=""><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US"><o:p></o:p></span></i></b></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Helvetica","sans-serif";"
lang="EN-US">For
more information about the course you can contact Celia van Gelder
(NBIC
Education) at <a class="moz-txt-link-abbreviated" href="mailto:celia.van.gelder@nbic.nl">celia.van.gelder@nbic.nl</a>.<span style="">
</span><o:p></o:p></span></p>
<br>
<br>
<small><font face="Helvetica, Arial, sans-serif"><b></b></font></small><span
style="font-size: 10pt; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US"><font face="Helvetica, Arial, sans-serif"><span style=""></span></font><o:p></o:p></span>
<pre class="moz-signature" cols="72">--
Dr. Celia W.G. van Gelder
Coordinator Education CMBI
Projectleader Education NBIC
tel. +31-(0)24-3666120
e-mail: <a class="moz-txt-link-abbreviated" href="mailto:C.vanGelder@cmbi.ru.nl">C.vanGelder@cmbi.ru.nl</a>
websites: <a class="moz-txt-link-abbreviated" href="http://www.cmbi.ru.nl">www.cmbi.ru.nl</a>, <a class="moz-txt-link-abbreviated" href="http://www.nbic.nl">www.nbic.nl</a>
Postal address:
CMBI 260
Radboud University Nijmegen-Medical Centre /NCMLS
PO Box 9101, 6500 HB Nijmegen
The Netherlands
</pre>
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