An update:<div><br></div><div>Now for NRG-CING, please see:</div><div><br></div><div><span class="Apple-style-span" style="border-collapse: collapse; color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; "><a href="http://nmr.cmbi.ru.nl/NRG-CING" target="_blank" style="color: rgb(17, 85, 204); ">http://nmr.cmbi.ru.nl/NRG-CING</a></span></div>
<div><br></div><div>Best,</div><div><br></div><div>Alan</div><div><br><div class="gmail_quote">On 3 April 2009 11:31, Alan <span dir="ltr"><<a href="mailto:alanwilter@gmail.com">alanwilter@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">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" target="_blank">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" target="_blank">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" target="_blank">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><span class="HOEnZb"><font color="#888888"><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" target="_blank">http://www.bio.cam.ac.uk/~awd28</a><<<br>
</font></span></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>Alan Wilter SOUSA da SILVA, DSc<div>Bioinformatician, UniProt - PANDA, EMBL-EBI<br>CB10 1SD, Hinxton, Cambridge, UK</div><div>+44 1223 49 4588</div><br>
</div>