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Fig. 5 | Algorithms for Molecular Biology

Fig. 5

From: StreAM-\(T_g\): algorithms for analyzing coarse grained RNA dynamics based on Markov models of connectivity-graphs

Fig. 5

Precomputation with different cut-offs. a Illustration of the the first frame of the TC-Aptamer simulation without TC th created with a cut-off of \(d=15 \) Å. Vertices (representing nucleotides) are colored in black and edges (representing interactions) in red. The edges belonging to the backbone are furthermore highlighted in black. Graphics were created using Pymol and R [39, 47]. b Number of \(\mathcal{T}(V')\) for a full computation of \(T_g(a)\) after selection with contact probability as function of cut-off d for three different adjacency sizes (\(k=3,4,5\)). The dashed lines show the number of matrices normally required for a full computation [\(k=3\), 262,080 matrices (green); \(k=4\) , 16,248,960 matrices (black); \(k=5\), 991,186,560 matrices (blue)]

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