Evaluation of the coarse-grained OPEP force field for protein-protein docking [0.03%]
用于蛋白质—蛋白质对接的粗粒化OPEP势场的评估
Philipp Kynast,Philippe Derreumaux,Birgit Strodel
Philipp Kynast
Background: Knowing the binding site of protein-protein complexes helps understand their function and shows possible regulation sites. The ultimate goal of protein-protein docking is the prediction of the three-dimensiona...
A biophysical model of supercoiling dependent transcription predicts a structural aspect to gene regulation [0.03%]
扭动依赖的转录生物物理模型预测了一个结构基因调控方面的问题
Christopher H Bohrer,Elijah Roberts
Christopher H Bohrer
Background: Transcription in Escherichia coli generates positive supercoiling in the DNA, which is relieved by the enzymatic activity of gyrase. Recently published experimental evidence suggests that transcription initiat...
α-synuclein-lanthanide metal ions interaction: binding sites, conformation and fibrillation [0.03%]
α-突触核蛋白-稀土金属离子的相互作用：结合位点、构象和细丝形成
Jia Bai,Zeting Zhang,Maili Liu et al.
Jia Bai et al.
Background: The pathological hallmark of Parkinson's disease is the deposition of cytoplasmic neuronal inclusions termed Lewy bodies. The major component of Lewy bodies is amyloid fibrils of α-synuclein. To investigate w...
Prediction of solution properties and dynamics of RNAs by means of Brownian dynamics simulation of coarse-grained models: Ribosomal 5S RNA and phenylalanine transfer RNA [0.03%]
运用粗粒化模型的布朗动力学模拟预测RNA溶液性质及构象运动：以核糖体5S RNA和苯丙氨酰转移RNA为例
Aarón Ayllón Benítez,José Ginés Hernández Cifre,Francisco Guillermo Díaz Baños et al.
Aarón Ayllón Benítez et al.
Background: The possibility of validating biological macromolecules with locally disordered domains like RNA against solution properties is helpful to understand their function. In this work, we present a computational sc...
PDE/ODE modeling and simulation to determine the role of diffusion in long-term and -range cellular signaling [0.03%]
基于PDE/ODE的建模与模拟确定扩散在长期和远距离细胞信号转导中的作用
Elfriede Friedmann
Elfriede Friedmann
Background: We study the relevance of diffusion for the dynamics of signaling pathways. Mathematical modeling of cellular diffusion leads to a coupled system of differential equations with Robin boundary conditions which ...
Copper-free click chemistry for attachment of biomolecules in magnetic tweezers [0.03%]
无铜点击化学在磁镊中的应用
Jorine M Eeftens,Jaco van der Torre,Daniel R Burnham et al.
Jorine M Eeftens et al.
Background: Single-molecule techniques have proven to be an excellent approach for quantitatively studying DNA-protein interactions at the single-molecule level. In magnetic tweezers, a force is applied to a biopolymer th...
Mathematical modelling of the automated FADU assay for the quantification of DNA strand breaks and their repair in human peripheral mononuclear blood cells [0.03%]
人外周血单个核细胞DNA链断裂及其修复的自动化FADU测定的数学建模
Michael Junk,Judy Salzwedel,Thilo Sindlinger et al.
Michael Junk et al.
Background: Cells continuously undergo DNA damage from exogenous agents like irradiation or genotoxic chemicals or from endogenous radicals produced by normal cellular metabolic activities. DNA strand breaks are one of th...
The biophysical nature of cells: potential cell behaviours revealed by analytical and computational studies of cell surface mechanics [0.03%]
细胞的生物物理性质：通过分析和计算研究细胞表面力学揭示的潜在细胞行为
Ramiro Magno,Verônica A Grieneisen,Athanasius Fm Marée
Ramiro Magno
Background: The biophysical characteristics of cells determine their shape in isolation and when packed within tissues. Cells can form regular or irregular epithelial structures, round up and form clusters, or deform and ...
Numerical calculation of protein-ligand binding rates through solution of the Smoluchowski equation using smoothed particle hydrodynamics [0.03%]
通过使用平滑粒子流体力学求解Smoluchowski方程来计算蛋白质配体结合速率的数值计算
Wenxiao Pan,Michael Daily,Nathan A Baker
Wenxiao Pan
Background: The calculation of diffusion-controlled ligand binding rates is important for understanding enzyme mechanisms as well as designing enzyme inhibitors. ...
A nucleotide-independent cyclic nitroxide label for monitoring segmental motions in nucleic acids [0.03%]
一种核苷酸独立的环状亚硝基标记物用于监测核酸中的片段运动
Phuong H Nguyen,Anna M Popova,Kálmán Hideg et al.
Phuong H Nguyen et al.
Background: Spin labels, which are chemically stable radicals attached at specific sites of a bio-molecule, enable investigations on structure and dynamics of proteins and nucleic acids using techniques such as site-direc...