title: Network visualization of conformational sampling during molecular dynamics simulation.
abstract: 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.
authors.affiliation: Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA.
authors.forename: Logan S
authors.initials: LS
authors.lastname: Ahlstrom
authors.forename: Joseph Lee
authors.initials: JL
authors.lastname: Baker
authors.forename: Kent
authors.initials: K
authors.lastname: Ehrlich
authors.forename: Zachary T
authors.initials: ZT
authors.lastname: Campbell
authors.forename: Sunita
authors.initials: S
authors.lastname: Patel
authors.forename: Ivan I
authors.initials: II
authors.lastname: Vorontsov
authors.forename: Florence
authors.initials: F
authors.lastname: Tama
authors.forename: Osamu
authors.initials: O
authors.lastname: Miyashita
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D057927:Hydrophobic and Hydrophilic Interactions; D056004:Molecular Dynamics Simulation; D025341:Principal Component Analysis; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D011506:Proteins
keywords: Clustering; Conformational sampling; Molecular dynamics simulation; Network visualization; Principal component analysis