Does anyone know any software or servers to calculate desolvation free energy between two proteins?

Juan Sebastian Lugo Ramos @Juan_Lugo_Ramos

02 February 2013 1 9K Report

I am trying to get thermodynamic measures for a protein protein docking, but I want to take as input my own generated pdb files. I have tried Fastcontact server and it works in several cases but not always.

Rogelio Rodríguez-Sotres

I know of no server specifically dealing with this problem, perhaps because calculations are time consuming. Please see this paper for a more detailed explanation of Molecular Dynamics free-energy perturbation methods employed to tackle this particular issue:

Tjong, H. & Zhou, H.-X.(2008). Prediction of Protein Solubility from Calculation of Transfer Free Energy. Biophysical journal, 95(6):2601-2609,

http://dx.doi.org/10.1371/journal.pone.0012483

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