We've recently announced iCing, which includes whatif as well. Please, take a look at <a href="http://nmr.cmbi.ru.nl/cing/Home.html">http://nmr.cmbi.ru.nl/cing/Home.html</a>.<div><br></div><div>If it happens that your complex is from NMR and deposit in PDB so you can find it here (<a href="http://nmr.cmbi.ru.nl/NRG-CING/index/index.html">http://nmr.cmbi.ru.nl/NRG-CING/index/index.html</a>) already evaluated.</div>
<div><br>Cheers,</div><div>Alan</div><div><br><div class="gmail_quote">On Fri, Apr 3, 2009 at 11:00, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><br>
Chih-Ying Lin wrote:<br>
><br>
><br>
><br>
> HI<br>
> The program WHATIF can perform a proper validation of the structure.<br>
> But, it is not free software.<br>
><br>
> Can anyone tell me how to test the protein structure manually or by Gromacs?<br>
><br>
> What is the criteria to determine the quality of the structure?<br>
<br>
That depends on your objective - but you have to define that. Ultimately<br>
some protein structure generated by a piece of software has to match in<br>
a relevant way the structure found in biological systems. What that<br>
means varies with what experimental information you have available.<br>
Various computational tools might assist in estimating that match.<br>
<br>
Mark<br>
<br></blockquote></div><br clear="all"><br>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>Department of Biochemistry, University of Cambridge.<br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>>><a href="http://www.bio.cam.ac.uk/~awd28">http://www.bio.cam.ac.uk/~awd28</a><<<br>
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