Hello Taiana
AREAIMOL can be used to calculate this kind of accessible area
difference, the easiest way to do it is to use the "Accessible Surface
Area" task in the "Structure Analysis" module of CCP4i.
In the interface window for this task, select the mode to "Run AreaIMol
to calculate [area differences due to ligand/subunit binding]". You must
then provide the PDB file with your coordinates, and define the
carbohydrate according by the chain ids in the file (in the "Ligand
Definition folder".
When the task is run in this mode it will calculate the difference in
area when the carbohydrate is present compared with when it is absent.
Hope that this helps, best wishes
Peter
Taiana Oliveira wrote:
> Hello everybody!
>
> I would like to know how to calculate how much accessible surface
> area is lost upon binding a determined carbohydrate to ConA lectin using
> SURFACE or AREAiMOL from CPP4.
> Thanks in advance for your help!
>
> Sincerely,
>
> --
> Taianá Maia de Oliveira
> Laboratório de Moléculas Biologicamente Ativas - Biomol-lab
> Departamento de Bioquímica e Biologia Molecular
> Univesidade Federal do Ceará
> Campus do Pici, s/n Bloco 907
> Caixa Postal 6043
> 60.455-970, Fortaleza-Ce, Brasil
> tel/fax: +55 85 33669818
--
___________________________________________________
Peter J Briggs, [log in to unmask] Tel: +44 1925 603826
CCP4, [log in to unmask] Fax: +44 1925 603825
http://www.ccp4.ac.uk/
Daresbury Laboratory, Daresbury, Warrington WA4 4AD
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