[gmx-users] Re: PDB structure quality

Alan alanwilter at gmail.com
Fri Apr 3 12:31:36 CEST 2009

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


On Fri, Apr 3, 2009 at 11:00, <gmx-users-request at 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.
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