[gmx-users] Re: PDB structure quality

[Alan]

An update:

Now for NRG-CING, please see:

http://nmr.cmbi.ru.nl/NRG-CING

Best,

Alan

On 3 April 2009 11:31, Alan <alanwilter at 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-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.
> >>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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