Hi,
As far as I understand the DeltaG given by PISA is kind of a "stability"
measure of the complex, not its binding DeltaG. It is also based on a
small part of the terms that contribute to a binding energy. I may be
wrong about that, but in any case, predicting a KD from a single
structure is something highly risky. The first thing you are leaving out
is entropy, which may be the most important term. You can estimate it
from normal modes analysis, but you would need to first minimize the
energy of the structure. Molecular dynamics (MD) people use a method
called MM-PBSA where they try to predict KDs from a number (hundreds or
more) of structures extracted from an MD simulation. The method is more
or less established, but the results are more meaningful in the context
of comparisons than for the prediction of absolute binding energies.
If you are only interested in some of the components of the binding
energies, like electrostatic and apolar binding and polar/apolar
solvation terms, you could use something like APBS
(http://www.poissonboltzmann.org/apbs/)
Cheers,
Miguel Ortiz Lombardía
Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:[log in to unmask]
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
Le 18/04/13 11:34, Boaz Shaanan a écrit :
> Hi,
>
> PISA have something like this, I think, or at least deltaG estimate.
>
> Boaz
>
> Boaz Shaanan, Ph.D.
> Dept. of Life Sciences
> Ben-Gurion University of the Negev
> Beer-Sheva 84105
> Israel
>
> E-mail: [log in to unmask]
> Phone: 972-8-647-2220 Skype: boaz.shaanan
> Fax: 972-8-647-2992 or 972-8-646-1710
>
>
>
>
>
> ________________________________________
> From: CCP4 bulletin board [[log in to unmask]] on behalf of Wei Liu [[log in to unmask]]
> Sent: Thursday, April 18, 2013 11:39 AM
> To: [log in to unmask]
> Subject: [ccp4bb] Program or server to predict Kd from complex structure
>
> Dear all,
>
> Does anyone know a program or web server that can predict Kd value between two proteins from a solved complex structure?
>
> Regards
> Wei
>
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