An update:
Now for NRG-CING, please see:
http://nmr.cmbi.ru.nl/NRG-CING
Best,
Alan
On 3 April 2009 11:31, Alan alanwil...@gmail.com wrote:
We've recently announced iCing, which includes whatif as well. Please,
take a look at http://nmr.cmbi.ru.nl/cing/Home.html.
If it happens that your complex is from NMR and deposit in PDB so you can
find it here (http://nmr.cmbi.ru.nl/NRG-CING/index/index.html) already
evaluated.
Cheers,
Alan
On Fri, Apr 3, 2009 at 11:00, gmx-users-requ...@gromacs.org wrote:
Chih-Ying Lin wrote:
HI
The program WHATIF can perform a proper validation of the structure.
But, it is not free software.
Can anyone tell me how to test the protein structure manually or by
Gromacs?
What is the criteria to determine the quality of the structure?
That depends on your objective - but you have to define that. Ultimately
some protein structure generated by a piece of software has to match in
a relevant way the structure found in biological systems. What that
means varies with what experimental information you have available.
Various computational tools might assist in estimating that match.
Mark
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
http://www.bio.cam.ac.uk/~awd28
--
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt - PANDA, EMBL-EBI
CB10 1SD, Hinxton, Cambridge, UK
+44 1223 49 4588
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