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StreAM- $$T_g$$ : Algorithms for Analyzing Coarse Grained RNA Dynamics Based on Markov Models of Connectivity-Graphs [chapter]

Sven Jager, Benjamin Schiller, Thorsten Strufe, Kay Hamacher
2016 Lecture Notes in Computer Science  
The intense computational demand for deriving the transition probability matrices prompted us to develop StreAM-T g , a stream-based algorithm for generating such Markov models of k-vertex adjacency matrices  ...  In this work, we present a new coarse grained representation of RNA dynamics. It is based on cliques and their patterns within adjacency matrices obtained from molecular dynamics simulations.  ...  Parts of this work have also been supported by the DFG, through the Cluster of Excellence cfaed as well as the CRC HAEC.  ... 
doi:10.1007/978-3-319-43681-4_16 fatcat:2dza5ypzwrgi3gpqcpdjmvsifa

StreAM- $$T_g$$ T g : algorithms for analyzing coarse grained RNA dynamics based on Markov models of connectivity-graphs

Sven Jager, Benjamin Schiller, Philipp Babel, Malte Blumenroth, Thorsten Strufe, Kay Hamacher
2017 Algorithms for Molecular Biology  
In 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.  ...  The intense computational demand for deriving the transition probability matrices prompted us to develop StreAM-T g , a streambased algorithm for generating such Markov models of k-vertex adjacency matrices  ...  In this study, we developed a new method StreAM-T g to analyze structural transitions, based on a coarse grained representation of RNA MD simulations, in order to gain insights into RNA dynamics.  ... 
doi:10.1186/s13015-017-0105-0 pmid:28572834 pmcid:PMC5450175 fatcat:psdsiouj7bgdlhf7qltadqj5he