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:[email protected] 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: [email protected] > Phone: 972-8-647-2220 Skype: boaz.shaanan > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > > ________________________________________ > From: CCP4 bulletin board [[email protected]] on behalf of Wei Liu > [[email protected]] > Sent: Thursday, April 18, 2013 11:39 AM > To: [email protected] > 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 >
