Accelerated Enveloping Distribution Sampling to Probe the Presence of Water Molecules.

ABSTRACT: Determining the presence of water molecules at protein-ligand interfaces is still a challenging task in free-energy calculations. The inappropriate placement of water molecules results in the stabilization of wrong conformational orientations of the ligand. With classical alchemical perturbation methods, such as thermodynamic integration (TI), it is essential to know the amount of water molecules in the active site of the respective ligands. However, the resolution of the crystal structure and the correct assignment of the electron density do not always lead to a clear placement of water molecules. In this work, we apply the one-step perturbation method named accelerated enveloping distribution sampling (AEDS) to determine the presence of water molecules in the active site by probing them

SUBMITTER: Gracia Carmona O 

PROVIDER: S-EPMC10269333 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature