sovent accesible surface area?<br><br><div class="gmail_quote">On Mon, May 18, 2009 at 11:09 AM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
stretching != swelling, e.g.<br>
<div><div></div><div class="h5"><br>
On Mon, May 18, 2009 at 10:46 AM, Bhanu <<a href="mailto:bhanuiitr@gmail.com">bhanuiitr@gmail.com</a>> wrote:<br>
> How about checking radius of gyration???<br>
><br>
> 2009/5/18 Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>
>><br>
>> Hi,<br>
>><br>
>> Well, I think 'swelling' is unambiguously, though roughly, defined as<br>
>> 'growing larger', which suggests that you'd have to look for an<br>
>> increase in volume. But how to do that, how to define the volume of<br>
>> the protein is still a matter of setting your criteria and finding the<br>
>> right tools to assess these. Not the simplest thing...<br>
>><br>
>> Cheers,<br>
>><br>
>> Tsjerk<br>
>><br>
>> On Mon, May 18, 2009 at 12:22 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
>> wrote:<br>
>> ><br>
>> ><br>
>> > Chih-Ying Lin wrote:<br>
>> >><br>
>> >> HI<br>
>> >> How can i know if the protein swell during the MD simulation?<br>
>> >><br>
>> >> What are those indications to "see" the swollen protein?<br>
>> >><br>
>> ><br>
>> > How do you define the term "swelling?" This again sounds like another<br>
>> > issue<br>
>> > on defining your own criteria for the expected behavior and reading the<br>
>> > manual about available analysis tools.<br>
>> ><br>
>> > -Justin<br>
>> ><br>
>> >> Thank you<br>
>> >> Lin<br>
>> >><br>
>> >><br>
>> >><br>
>> >> ------------------------------------------------------------------------<br>
>> >><br>
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>> > ========================================<br>
>> ><br>
>> > Justin A. Lemkul<br>
>> > Ph.D. Candidate<br>
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>> > Department of Biochemistry<br>
>> > Virginia Tech<br>
>> > Blacksburg, VA<br>
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>><br>
>><br>
>><br>
>> --<br>
>> Tsjerk A. Wassenaar, Ph.D.<br>
>> Junior UD (post-doc)<br>
>> Biomolecular NMR, Bijvoet Center<br>
>> Utrecht University<br>
>> Padualaan 8<br>
>> 3584 CH Utrecht<br>
>> The Netherlands<br>
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><br>
><br>
><br>
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<br>
<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
Junior UD (post-doc)<br>
Biomolecular NMR, Bijvoet Center<br>
Utrecht University<br>
Padualaan 8<br>
3584 CH Utrecht<br>
The Netherlands<br>
P: +31-30-2539931<br>
F: +31-30-2537623<br>
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</div></div></blockquote></div><br>