Modeler is a program that can do this sort of thing (build in missing
residues) from the sequence and structures without the missing residues
or homologous structures. <br><br><div><span class="gmail_quote">On 12/28/05, <b class="gmail_sendername">Kaasi Sridhara</b> <<a href="mailto:research.gromacs@gmail.com">research.gromacs@gmail.com</a>> wrote:</span>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">I am unable to find resonable sidechains to be added, as Tsjerk and
yourself mentioned. I will try to look at the molecule builder
programs available, try to see what "reasonable" sidechains can be
added, and proceed.
<br>I am not "that" familiar with biochemistry, as myself being an electrical engineer, but working in bioelectrics simulations.<br>Thanks for the suggestions, I will get back to you once I do my homework properly.
<br>Thanks again....<br><div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br><div><span><span class="gmail_quote">On 12/28/05,
<b class="gmail_sendername">Mark Abraham</b> <<a href="mailto:mark.abraham@anu.edu.au" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">mark.abraham@anu.edu.au</a>> wrote:</span></span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<span>
> Did anyone tried to work on this problem earlier, or can anyone suggest<br>> how<br>> to deal with this problem of adding missing residues.<br><br></span>One approach is to use some visual molecule builder program to pick a
<br>chemically reasonable starting point for each of the side chains you have<br>to build and do an energy minimisation on that (preferably restraining the<br>atoms you haven't fabricated to their positions in the PDB file). You
<br>would want to be intelligent about side chains in active sites or pores or<br>whatever.<br><br>Mark<br><br><br>_______________________________________________<br>gmx-users mailing list<br><a href="mailto:gmx-users@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
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<a href="mailto:gmx-users-request@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users-request@gromacs.org</a>.<br></blockquote></div><span><br><br clear="all"><br>-- <br>
Viswanadham Sridhara,<br>Graduate Research Assistant,<br>Old Dominion University, "VIRGINIA".
<br>
</span></blockquote></div><br>
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