Network visualization of conformational sampling during molecular dynamics simulation

作者：Ahlstrom Logan S; Baker Joseph Lee; Ehrlich Kent; Campbell Zachary T; Patel Sunita; Vorontsov Ivan I; Tama Florence; Miyashita Osamu^*

来源：Journal of Molecular Graphics and Modelling, 2013, 46: 140-149.

DOI：10.1016/j.jmgm.2013.10.003

• Network visualization
• Molecular dynamics simulation
• Conformational sampling
• Clustering
• Principal component analysis

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.

• 出版日期2013-11