Çifii, GülşahAviyente, ViktoryaAkten, Ebru DemetMonard, Gerald2019-06-272019-06-27201710920-654X1573-49510920-654X1573-4951https://hdl.handle.net/20.500.12469/341https://doi.org/10.1007/s10822-017-0024-7In a first step in the discovery of novel potent inhibitor structures for the PDE4B family with limited side effects we present a protocol to rank newly designed molecules through the estimation of their IC values. Our protocol is based on reproducing the linear relationship between the logarithm of experimental IC values [(IC)] and their calculated binding free energies (). From 13 known PDE4B inhibitors we show here that (1) binding free energies obtained after a docking process by AutoDock are not accurate enough to reproduce this linear relationship(2) MM-GB/SA post-processing of molecular dynamics (MD) trajectories of the top ranked AutoDock pose improves the linear relationship(3) by taking into account all representative structures obtained by AutoDock and by averaging MM-GB/SA computations on a series of 40 independent MD trajectories a linear relationship between (IC) and the lowest is achieved with R-2 = 0.944 .eninfo:eu-repo/semantics/openAccessPDE4BIC50Molecular dockingMolecular dynamicsMM-GB/SAArticle563575631WOS:00040368970000410.1007/s10822-017-0024-72-s2.0-85019924963Q2Q228534194