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| - Including Tightly-Bound Water Molecules in de Novo Drug Design. Exemplificationthrough the in Silico Generation of Poly(ADP-ribose)polymerase Ligands
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| - Different strategies for the in silico generation of ligand molecules in the binding site of poly(ADP-ribose)polymerase (PARP) were studied in order to observe the effect of the targeting and displacement of tightlybound water molecules. Several molecular scaffolds were identified as having better interactions in thebinding site when targeting one or two tightly bound water molecules in the NAD binding site. Energycalculations were conducted in order to assess the ligand−protein and ligand−water−protein interactionsof different functional groups of the generated ligands. These calculations were used to evaluate the energeticconsequences of the presence of tightly bound water molecules and to identify those that contribute favorablyto the binding of ligands.
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