Application of the Movable Type Free Energy Method to the Caspase-Inhibitor BindingAffinity Study.

ABSTRACT: Many studies have provided evidence suggesting that caspases not only contribute to the neurodegeneration associated with Alzheimer's disease (AD) but also play essential roles in promoting the underlying pathology of this disease. Studies regarding the caspase inhibition draw researchers' attention through time due to its therapeutic value in the treatment of AD. In this work, we apply the "Movable Type" (MT) free energy method, a Monte Carlo sampling method extrapolating the binding free energy by simulating the partition functions for both free-state and bound-state protein and ligand configurations, to the caspase-inhibitor binding affinity study. Two test benchmarks are introduced to examine the robustness and sensitivity of the MT method concerning the caspase inhibition complexing.

SUBMITTER: Xue S 

PROVIDER: S-EPMC6801467 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature