Partially something works - dock management and so on. Deleted the old dDock from programs folder, reboot, dumped the beta into the programs, rebooted. Changing the color/layout of the dock or making it transparent does not work. These studies demonstrate the utility of the LigScore2 scoring function and that LibDock as a feature directed docking method performs as well as docking programs that use genetic/growing and Monte Carlo driven algorithms. I can't get cDock to show indicators for running apps. The results for LibDock accuracy and ligand retrieval in virtual screening are compared to 10 other docking and scoring programs. In both studies the LigScore2 scoring function enhanced the retrieval of crystallographic poses or active compounds in comparison with the results obtained using the DJD scoring function. LibDock retrieved at least 20% of active compounds in the top 10% of screened ligands for four of the eight targets in the virtual screening protocol. For six out of eight targets at least 30% of the ligands were docked within a root-mean-square difference (RMSD) of 2.0 A for the crystallographic poses when the LigScore2 scoring function was used. This study was conducted using DJD scoring, and poses were rescored using all available scoring functions in the Accelrys LigandFit module, including LigScore2. Its faster, has more modern ports, can push more resolution to external displays. Proteins 2001, 43, 113-124) and LigScore2 (Krammer, A. The Surface Dock 2 improves upon the original Surface Dock in just about every way. Docking experiments were performed to assess both the accuracy in reproducing the binding mode of the ligand and the retrieval of active compounds in a virtual screening protocol using both the DJD (Diller, D. The performance of the site-features docking algorithm LibDock has been evaluated across eight GlaxoSmithKline targets as a follow-up to a broad validation study of docking and scoring software (Warren, G.
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