Publication:molecular pharmaceutics
Authors:Dr. Yuriy Abramov, Dr. Guangxu Sun et al.
Date:Jan. 13, 2020
Although there are a number of computational approaches available for the aqueous solubility prediction, a majority of those models rely on the existence of a training set of thermodynamic solubility measurements or/and fail to accurately account for the lattice packing contribution to the solubility. The main focus of this study is the validation of the application of a physics-based aqueous solubility approach…
Publication:Journal of Computational Chemistry
Authors:Dr. Shuai Liu, Dr. Mingjun Yang et al.
Date:Nov. 13, 2019
Pairwise‐based methods such as the free energy perturbation (FEP) method have been widely deployed to compute the binding free energy differences between two similar host–guest complexes. The calculated pairwise free energy difference is either directly adopted or transformed to absolute…
Publication:Crystal Growth Design
Authors:Dr. Yuriy Abramov, Dr. Guangxu Sun
Date:Oct. 17, 2019
The focus of this study is an estimation of uncertainty of solid-form transition temperature (Ttr) prediction based on modern virtual polymorph screening calculations. That was done through error propagation, utilizing estimated uncertainties of the relative free energy predictions at 0 K as well as of finite-temperature contribution to the polymorphic relative free energy…
Publication:The Journal of Chemical Physics
Authors:Dr. M. A. Bellucci et al.
Date:March 5, 2019
Li and co-workers [Li et al., J. Chem. Phys. 146, 214110 (2017)] have recently proposed a methodology to compute the solubility of molecular compounds from first principles, using molecular dynamics simulations. We revise and further explore their methodology that was originally applied to nap…
Publication:The Journal of Chemical Physics
Authors:Dr. Huimin Cheng, Dr. Dong Fang, Dr Mingjun Yang et al.
Date:Jan. 31, 2019
Free energy calculations for chemical reactions with a steep energy barrier require well defined reaction coordinates (RCs). However, when multiple parallel channels exist along selected RC, the application of conventional enhanced samplings is difficult to generate correct sampling within li…
Publication:Catalysis Science & Technology
Authors:Dr. Mingjun Yang et al.
Date:Dec. 6, 2018
Elucidation of the role of entropy in enzymatic reactions can be utilized in the de novo design of enzymes or protein engineering. Recently, the change in entropy in the enzyme-catalyzed chorismate mutase reaction brought about uncertainty as a result of an experiment using PchB, in …