QM/MM-PB/SA scoring of the interaction strength between Akt kinase and apigenin analogues.Identification of small-molecule compounds that can bind specifically and stably to protein targets of biological interest is a challenge task in structure-based drug design.  In the current study, we raised the rigorous quantum mechanics/molecular mechanics in combination with semi-empirical Poisson-Boltzmann/surface area (QM/MM-PB/SA) as an efficient strategy to characterize the intermolecular interaction between Akt kinase and its small-molecule ligands, although this hybrid approach is computationally expensive as compared to those empirical methods.  In a round of experimental activity reproduction test based on a set of known Akt-inhibitor complexes, QM/MM-PB/SA has been shown to perform much better than two widely used scoring functions as well as the sophisticated MM-PB/SA analysis with or without improvement by molecular dynamics (MD) simulations.  Next, the QM/MM-PB/SA was employed to screen for strong Akt binders from an apigenin analogue set. 
QM/MM-PB/SA
QM/MM-PB/SA scoring of the interaction strength between Akt kinase and apigenin analogues.Identification of small-molecule compounds that can bind specifically and stably to protein targets of biological interest is a challenge task in structure-based drug design.  In the current study, we raised the rigorous quantum mechanics/molecular mechanics in combination with semi-empirical Poisson-Boltzmann/surface area (QM/MM-PB/SA) as an efficient strategy to characterize the intermolecular interaction between Akt kinase and its small-molecule ligands, although this hybrid approach is computationally expensive as compared to those empirical methods.  In a round of experimental activity reproduction test based on a set of known Akt-inhibitor complexes, QM/MM-PB/SA has been shown to perform much better than two widely used scoring functions as well as the sophisticated MM-PB/SA analysis with or without improvement by molecular dynamics (MD) simulations.  Next, the QM/MM-PB/SA was employed to screen for strong Akt binders from an apigenin analogue set. 
QM/MM-PB/SA
QM/MM-PB/SA scoring of the interaction strength between Akt kinase and apigenin analogues.Identification of small-molecule compounds that can bind specifically and stably to protein targets of biological interest is a challenge task in structure-based drug design.  In the current study, we raised the rigorous quantum mechanics/molecular mechanics in combination with semi-empirical Poisson-Boltzmann/surface area (QM/MM-PB/SA) as an efficient strategy to characterize the intermolecular interaction between Akt kinase and its small-molecule ligands, although this hybrid approach is computationally expensive as compared to those empirical methods.  In a round of experimental activity reproduction test based on a set of known Akt-inhibitor complexes, QM/MM-PB/SA has been shown to perform much better than two widely used scoring functions as well as the sophisticated MM-PB/SA analysis with or without improvement by molecular dynamics (MD) simulations.  Next, the QM/MM-PB/SA was employed to screen for strong Akt binders from an apigenin analogue set. 
QM/MM-PB/SA
QM/MM-PB/SA scoring of the interaction strength between Akt kinase and apigenin analogues.Identification of small-molecule compounds that can bind specifically and stably to protein targets of biological interest is a challenge task in structure-based drug design.  In the current study, we raised the rigorous quantum mechanics/molecular mechanics in combination with semi-empirical Poisson-Boltzmann/surface area (QM/MM-PB/SA) as an efficient strategy to characterize the intermolecular interaction between Akt kinase and its small-molecule ligands, although this hybrid approach is computationally expensive as compared to those empirical methods.  In a round of experimental activity reproduction test based on a set of known Akt-inhibitor complexes, QM/MM-PB/SA has been shown to perform much better than two widely used scoring functions as well as the sophisticated MM-PB/SA analysis with or without improvement by molecular dynamics (MD) simulations.  Next, the QM/MM-PB/SA was employed to screen for strong Akt binders from an apigenin analogue set. 
QM/MM-PB/SA
QM/MM-PB/SA scoring of the interaction strength between Akt kinase and apigenin analogues.Identification of small-molecule compounds that can bind specifically and stably to protein targets of biological interest is a challenge task in structure-based drug design.  In the current study, we raised the rigorous quantum mechanics/molecular mechanics in combination with semi-empirical Poisson-Boltzmann/surface area (QM/MM-PB/SA) as an efficient strategy to characterize the intermolecular interaction between Akt kinase and its small-molecule ligands, although this hybrid approach is computationally expensive as compared to those empirical methods.  In a round of experimental activity reproduction test based on a set of known Akt-inhibitor complexes, QM/MM-PB/SA has been shown to perform much better than two widely used scoring functions as well as the sophisticated MM-PB/SA analysis with or without improvement by molecular dynamics (MD) simulations.  Next, the QM/MM-PB/SA was employed to screen for strong Akt binders from an apigenin analogue set. 
QM/MM-PB/SA
QM/MM-PB/SA scoring of the interaction strength between Akt kinase and apigenin analogues.Identification of small-molecule compounds that can bind specifically and stably to protein targets of biological interest is a challenge task in structure-based drug design.  In the current study, we raised the rigorous quantum mechanics/molecular mechanics in combination with semi-empirical Poisson-Boltzmann/surface area (QM/MM-PB/SA) as an efficient strategy to characterize the intermolecular interaction between Akt kinase and its small-molecule ligands, although this hybrid approach is computationally expensive as compared to those empirical methods.  In a round of experimental activity reproduction test based on a set of known Akt-inhibitor complexes, QM/MM-PB/SA has been shown to perform much better than two widely used scoring functions as well as the sophisticated MM-PB/SA analysis with or without improvement by molecular dynamics (MD) simulations.  Next, the QM/MM-PB/SA was employed to screen for strong Akt binders from an apigenin analogue set. 
QM/MM-PB/SA