Network visualization of conformational sampling during molecular dynamics simulation

•Network visualization aids analysis of large molecular dynamics trajectories.•Networks reveal the connectivity between dominant conformational states.•Compare network visualization against clustering and principal component analysis.•Networks facilitate functional conclusions for several protein simulations. Effective data reduction methods are necessary for uncovering the inherent conformational relationships present in large molecular dynamics (MD) trajectories. Clustering algorithms provide a means to interpret the conformational sampling of molecules during simulation by grouping trajectory snapshots into a few subgroups, or clusters, but the relationships between the individual clusters may not be readily understood. Here we show that network analysis can be used to visualize the dominant conformational states explored during simulation as well as the connectivity between them, providing a more coherent description of conformational space than traditional clustering techniques alone. We compare the results of network visualization against 11 clustering algorithms and principal component conformer plots. Several MD simulations of proteins undergoing different conformational changes demonstrate the effectiveness of networks in reaching functional conclusions.