Huiying Chu

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The free energy calculation library PLUMED has been incorporated into the OpenMM simulation toolkit, with the purpose to perform enhanced sampling MD simulations using the AMOEBA polarizable force field on GPU platform. Two examples, (I) the free energy profile of water pair separation (II) alanine dipeptide dihedral angle free energy surface in explicit(More)
Classical molecular dynamic (MD) simulation of membrane proteins faces significant challenges in accurately reproducing and predicting experimental observables such as ion conductance and permeability due to its incapability of precisely describing the electronic interactions in heterogeneous systems. In this work, the free energy profiles of K(+) and Na(+)(More)
Bone homeostasis is maintained by formation and destruction of bone, which are two processes tightly coupled and controlled. Targeting both stimulation on bone formation and suppression on bone resorption becomes a promising strategy for treating osteoporosis. In this study, we examined the effect of wedelolactone, a natural product from Ecliptae herba, on(More)
Metabolomics has shown significant potential in identifying small molecules specific to tumor phenotypes. In this study we analyzed resected tissue metabolites using capillary electrophoresis-mass spectrometry and found that tissue hypotaurine levels strongly and positively correlated with glioma grade. In vitro studies were conducted to show that(More)
Dramatic functional changes of enzyme usually require scores of alterations in amino acid sequence. However, in the case of guanylate kinase (GK), the functional novelty is induced by a single (S→P) mutation, leading to the functional transition of the enzyme from a phosphoryl transfer kinase into a phosphorprotein interaction domain. Here, by using(More)
In this work, we aim at optimizing the performance of the anisotropic GBEMP model, which adopts a framework by combining a Gay-Berne (GB) anisotropic potential with an electric multipole (EMP) potential, in simulating a DMPC lipid bilayer in an implicit solvent model. First, the Gay-Berne parameters were initially obtained by fitting to atomistic profiles(More)
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