An Iterative Bézier Method for Fitting Beta-sheet Component of a Cryo-EM Density Map [0.03%]
一种迭代贝塞尔方法，用于配合冷冻电镜密度图中的β折叠组件
Michael Poteat,Jing He
Michael Poteat
Cryo-electron microscopy (Cryo-EM) is a powerful technique to produce 3-dimensional density maps for large molecular complexes. Although many atomic structures have been solved from cryo-EM density maps, it is challenging to derive atomic s...
A Knot Polynomial Invariant for Analysis of Topology of RNA Stems and Protein Disulfide Bonds [0.03%]
用于分析RNA茎和蛋白质二硫键拓扑结构的结多项式不变量
Wei Tian,Xue Lei,Louis H Kauffman et al.
Wei Tian et al.
Knot polynomials have been used to detect and classify knots in biomolecules. Computation of knot polynomials in DNA and protein molecules have revealed the existence of knotted structures, and provided important insight into their topologi...
Nonlocal Electrostatics in Spherical Geometries Using Eigenfunction Expansions of Boundary-Integral Operators [0.03%]
基于边界积分算子本征展开的球形几何中非局域静电学
Jaydeep P Bardhan,Matthew G Knepley,Peter Brune
Jaydeep P Bardhan
In this paper, we present an exact, infinite-series solution to Lorentz nonlocal continuum electrostatics for an arbitrary charge distribution in a spherical solute. Our approach relies on two key steps: (1) re-formulating the PDE problem u...
Analysis of fast boundary-integral approximations for modeling electrostatic contributions of molecular binding [0.03%]
快速边界积分法在建模分子结合静电效应中的分析与应用
Amelia B Kreienkamp,Lucy Y Liu,Mona S Minkara et al.
Amelia B Kreienkamp et al.
We analyze and suggest improvements to a recently developed approximate continuum-electrostatic model for proteins. The model, called BIBEE/I (boundary-integral based electrostatics estimation with interpolation), was able to estimate elect...
High-order fractional partial differential equation transform for molecular surface construction [0.03%]
基于高阶分数阶偏微分方程变换的分子表面构建方法研究
Langhua Hu,Duan Chen,Guo-Wei Wei
Langhua Hu
Fractional derivative or fractional calculus plays a significant role in theoretical modeling of scientific and engineering problems. However, only relatively low order fractional derivatives are used at present. In general, it is not obvio...
Multi-core CPU or GPU-accelerated Multiscale Modeling for Biomolecular Complexes [0.03%]
多核CPU与GPU加速的生物分子复合物多层次模型模拟方法研究
Tao Liao,Yongjie Zhang,Peter M Kekenes-Huskey et al.
Tao Liao et al.
Multi-scale modeling plays an important role in understanding the structure and biological functionalities of large biomolecular complexes. In this paper, we present an efficient computational framework to construct multi-scale models from ...
Chuan Li,Lin Li,Marharyta Petukh et al.
Chuan Li et al.
This review outlines the recent progress made in developing more accurate and efficient solutions to model electrostatics in systems comprised of bio-macromolecules and nano-objects, the last one referring to objects that do not have biolog...