High-Resolution Coarse-Grained Modeling Using Oriented Coarse-Grained Sites
نویسندگان
چکیده
منابع مشابه
High-Resolution Coarse-Grained Modeling Using Oriented Coarse-Grained Sites.
We introduce a method to bring nearly atomistic resolution to coarse-grained models, and we apply the method to proteins. Using a small number of coarse-grained sites (about one per eight atoms) but assigning an independent three-dimensional orientation to each site, we preferentially integrate out stiff degrees of freedom (bond lengths and angles, as well as dihedral angles in rings) that are ...
متن کاملCoarse-grained modeling of mucus barrier properties.
We designed a simple coarse-grained model of the glycocalyx layer, or adhesive mucus layer (AML), covered by mucus gel (luminal mucus layer) using a polymer lattice model and stochastic sampling (replica exchange Monte Carlo) for canonical ensemble simulations. We assumed that mucin MUC16 is responsible for the structural properties of the AML. Other mucins that are much smaller in size and les...
متن کاملCoarse Grained Molecular Kinetics
The dynamic behavior of molecules can often be described by Markov processes. From computational molecular simulations one can derive transition rates or transition probabilities between subsets of the discretized conformational space. On the basis of this dynamic information, the spatial subsets are combined into a small number of so-called metastable molecular conformations. This is done by c...
متن کاملCoarse-grained modeling of DNA curvature.
The interaction of DNA with proteins occurs over a wide range of length scales, and depends critically on its local structure. In particular, recent experimental work suggests that the intrinsic curvature of DNA plays a significant role on its protein-binding properties. In this work, we present a coarse grained model of DNA that is capable of describing base-pairing, hybridization, major and m...
متن کاملMultiscale modeling of coarse-grained macromolecular liquids.
A first-principle multiscale modeling approach is presented, which is derived from the solution of the Ornstein-Zernike equation for the coarse-grained representation of polymer liquids. The approach is analytical, and for this reason is transferable. It is here applied to determine the structure of several polymeric systems, which have different parameter values, such as molecular length, mono...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Journal of Chemical Theory and Computation
سال: 2015
ISSN: 1549-9618,1549-9626
DOI: 10.1021/ct500881x