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Baseline absolute alchemical binding predictions for UPA inhibitors. Evaluating the effects of simulation with 150 mM salt alone, deprotonated ligands alone, and with 150 mM salt and deprotonated ligands combined (1DOF All-HIP) on the baseline condition (fully protonated ligands, counterions added only up to neutralize system charge, and 1DOF restraints). The highest performance is observed with the 1DOF All-HIP condition with RMSE 2.50 kcal/mol and Pearson correlation 0.51.
