Method
Introduction
SenseNet (``Structure ENSEmble NETworks'') maps structure ensembles of biomolecules to atom interaction networks and provides functions for their analysis and visualization. It is available as a plugin for the free network visualization software Cytoscape.
Protein structures are frequently analysed to gain insights into the effects of ligand binding, residue mutations or conformational changes. In contrast to isolated structures generated by crystallography or other experimental sources, ensembles obtained from Molecular Dynamics (MD) provide additional information such as interaction lifetimes or correlation between conformations, allowing to investigate dynamic properties of biomolecules. In a structure ensemble network, each node represents one or a group of atoms while edges correspond to the interactions between these atoms (e.g. hydrophobic contacts or hydrogen bonds). Each edge is associated with a 'timeline' which indicates the presence of an interaction for each structure in the ensemble. Analysis functions are provided to extract information from these timelines and map results to network nodes and edges. Finally, SenseNet offers comprehensive visualization functions for side-by-side analyses of networks and 3D structures.
Publications
If you use SenseNet in your work, please cite
Schneider M, Antes I. SenseNet, a tool for analysis of protein structure networks obtained from molecular dynamics simulations. (2022) PLOS ONE 17(3): e0265194.
https://doi.org/10.1371/journal.pone.0265194
More information about the usage of SenseNet and its implemented algorithms can be found in the following application studies (TBA).