Solvent docking

YETI is a force held designed for the accurate representation of nonbonded interactions. It is most often used for modeling interactions between biomolecules and small substrate molecules. It is not designed for molecular geometry optimization so researchers often optimize the molecular geometry with some other force held, such as AMBER, then use YETI to model the docking process. Recent additions to YETI are support for metals and solvent effects. 

Totrov, M. Accurate and efficient generalized Bom model based on solvent accessibility derivation and application for logP octanol/water prediction and flexible peptide docking, f Comput. Chem. 2004, 25, 609-619. 

In the preferential interaction model, the equilibrium association constant, K.ISVIC, for a peptide docked to a RPC sorbent can be related via eq 6 to the changes in the preferential interaction of the solvent and water with the peptide P- the ligands L, and the peptide-ligand complex PtL as a function of solvent concentration, [3]m. The effect of preferential hydration/solvation of a peptide on k can be represented in terms of the following expression t85l... 

Tertiary alcohols are very unreactive toward hydrolases. There are, however, exceptions. Some enzymes have a certain amino acid motif located in the oxyanion binding pocket that allows the docking of space-demanding alcohols such as tertiary ones into the acylated enzyme [104]. One such hydrolase is Candida antarctica lipase A (CALA), which has been found to catalyze the acylation of the tertiary 2-phenyl-3-butyn-2-ol rac-110 by vinyl acetate in organic solvents. Thus efficient resolution of 110 was achieved in isooctane at room temperature (Scheme 4.34) [105]. 

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