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  • Title: Assessing protein kinase selectivity with molecular dynamics and mm-pbsa binding free energy calculations.
    Author: Muzzioli E, Del Rio A, Rastelli G.
    Journal: Chem Biol Drug Des; 2011 Aug; 78(2):252-9. PubMed ID: 21585710.
    Abstract:
    An application of molecular dynamics and molecular mechanics Poisson-Boltzmann surface area techniques to the prediction of protein kinase inhibitor selectivity is presented. A highly active and selective ERK2 inhibitor was placed in equivalent orientations in five different protein kinases (SRC, LCK, GSK3, JNK3 and Aurora-A). Binding free energies were then computed with the molecular mechanics Poisson-Boltzmann surface area approach using 15 nanosecond fully solvated molecular dynamics trajectories of the corresponding protein-ligand complexes. The results show correlation with experimentally determined selectivities and provide useful insights into the underlying structural determinants for selectivity.
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