StreAM-... formula ...: algorithms for analyzing coarse grained RNA dynamics based on Markov models of connectivity-graphs

机译：StreAM-...公式...：基于连通图的马尔可夫模型的粗粒RNA动力学分析算法

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BackgroundIn this work, we present a new coarse grained representation of RNA dynamics. It is based on adjacency matrices and their interactions patterns obtained from molecular dynamics simulations. RNA molecules are well-suited for this representation due to their composition which is mainly modular and assessable by the secondary structure alone. These interactions can be represented as adjacency matrices of k nucleotides. Based on those, we define transitions between states as changes in the adjacency matrices which form Markovian dynamics. The intense computational demand for deriving the transition probability matrices prompted us to develop StreAM-Tg, a stream-based algorithm for generating such Markov models of k-vertex adjacency matrices representing the RNA.

机译：背景在这项工作中，我们提出了一种新的粗略的RNA动力学表示方法。它基于邻接矩阵及其从分子动力学模拟获得的相互作用模式。由于RNA分子的组成主要是模块化的，并且仅通过二级结构即可评估，因此非常适合此表示形式。这些相互作用可以表示为k个核苷酸的邻接矩阵。基于这些，我们将状态之间的过渡定义为形成马尔可夫动力学的邻接矩阵的变化。对导出过渡概率矩阵的大量计算需求促使我们开发StreAM-Tg，这是一种基于流的算法，用于生成代表RNA的k顶点邻接矩阵的此类Markov模型。

著录项

期刊名称 Algorithms for Molecular Biology : AMB
作者
Sven Jager; Benjamin Schiller; Philipp Babel; Malte Blumenroth; Thorsten Strufe; Kay Hamacher;
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作者单位

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年(卷),期 2017(12),-1
年度 2017
页码 15
总页数 16
原文格式 PDF
正文语种
中图分类应用微生物学;生化遗传学;生化药理学;
关键词
RNA Markovian dynamics Dynamic graphs Molecular dynamics Coarse graining Synthetic biology;

机译：RNA;马尔可夫动力学;动力学图;分子动力学;粗粒化;合成生物学;

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专利

1. StreAM- $$T_g$$ T g : algorithms for analyzing coarse grained RNA dynamics based on Markov models of connectivity-graphs [J] . Sven Jager, Benjamin Schiller, Philipp Babel, Algorithms for Molecular Biology . 2017,第1期

机译：StreAM- $$ T_g $$ T g：基于连通图的马尔可夫模型分析粗粒RNA动力学的算法
2. The mechanism of RNA base fraying: Molecular dynamics simulations analyzed with core-set Markov state models [J] . Pinamonti Giovanni, Paul Fabian, Noe Frank, The Journal of Chemical Physics . 2019,第15期

机译：RNA基础磨损的机制：用核心设定的马尔可夫状态模型分析分子动力学模拟
3. The mechanism for the complexation and dissociation between siRNA and PMAL: a molecular dynamics simulation study based on a coarse-grained model [J] . Lu Yanfei, Li Jipeng, Lu Diannan Molecular simulation . 2017,第13a16期

机译：siRNA和PMAL络合与解离的机制：基于粗粒模型的分子动力学模拟研究
4. StreAM-T_g: Algorithms for Analyzing Coarse Grained RNA Dynamics Based on Markov Models of Connectivity-Graphs [C] . Sven Jager, Benjamin Schiller, Thorsten Strufe, International workshop on algorithms in bioinformatics . 2016

机译：StreAM-T_g：基于连通图的马尔可夫模型的粗粒RNA动力学分析算法
5. Multiscale Particle-Based Modeling of Mechanotransduction Process in Flow-Induced Platelet Activation using Dissipative Particle Dynamics and Coarse Grained Molecular Dynamics. [D] . Gao, Chao. 2016

机译：基于耗散粒子动力学和粗粒分子动力学的流动诱导血小板活化的机械转导过程的多尺度粒子建模。
6. Markov state modeling and dynamical coarse-graining via discrete relaxation path sampling [O] . B. Fačkovec, E. Vanden-Eijnden, D. J. Wales -1

机译：马尔可夫状态建模和通过离散弛豫路径采样进行的动态粗粒度
7. StreAM-Tg : algorithms for analyzing coarse grained RNA dynamics based on Markov models of connectivity-graphs [O] . Jager, Sven, Schiller, Benjamin, Babel, Philipp, 2017

机译：StreAM-Tg：基于连通图的马尔可夫模型的粗粒RNA动力学分析算法

StreAM-... formula ...: algorithms for analyzing coarse grained RNA dynamics based on Markov models of connectivity-graphs

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