Setup

  • Protein: pNB-Esterase 13
  • 490 amino acids
  • 50 ns, snapshot every 25 ps => 20,000 Frames
  • Distance thresholds: 7,8,..,14 Angstrom
  • Coordinates (double, integer)

Graph generation

Analysis results: undirected 4-vertex motifs

Visualizations

StreAM-Tg : Algorithms for Analyzing Coarse Grained RNA Dynamics based on Markov Models of Connectivity-GraphsStreAM-Tg : Algorithms for Analyzing Coarse Grained RNA Dynamics based on Markov Models of Connectivity-Graphs
Sven Jager, Benjamin Schiller, Thorsten Strufe, Kay Hamacher
In: Proceedings of the 16th Workshop on Algorithms in Bioinformatics (WABI 2016)
StreaM - a Stream-based Algorithm for Counting Motifs in Dynamic GraphsStreaM - a Stream-based Algorithm for Counting Motifs in Dynamic Graphs
Benjamin Schiller, Sven Jager, Kay Hamacher, Thorsten Strufe
In: Proceedings of the 2nd International Conference on Algorithms for Computational Biology (AlCoB 2015)