Cluster analysis of molecular simulation trajectories for systems where both conformation and orientation of the sampled states are important.
Clustering methods have been widely used to group together similar conformational states from molecular simulations of biomolecules in solution. For applications such as the interaction of a protein with a surface, the orientation of the protein relative to the surface is also an important clustering parameter because of its potential effect on adsorbed-state bioactivity. This study presents cluster analysis methods that are specifically designed for systems where both molecular orientation and conformation are important, and the methods are demonstrated using test cases of adsorbed proteins for validation. Additionally, because cluster analysis can be a very subjective process, an objective procedure for identifying both the optimal number of clusters and the best clustering algorithm to be applied to analyze a given dataset is presented. The method is demonstrated for several agglomerative hierarchical clustering algorithms used in conjunction with three cluster validation techniques. © 2016 Wiley Periodicals, Inc.
Department of Bioengineering, 501 Rhodes Engineering Research Center, Clemson University, Clemson, South Carolina, 29634.
Tigran M
TM
Abramyan
Department of Bioengineering, 501 Rhodes Engineering Research Center, Clemson University, Clemson, South Carolina, 29634.
James A
JA
Snyder
Department of Bioengineering, 501 Rhodes Engineering Research Center, Clemson University, Clemson, South Carolina, 29634.
Aby A
AA
Thyparambil
Department of Chemistry 369 Hunter Laboratory, Clemson University, Clemson, South Carolina, 29634.
Steven J
SJ
Stuart
Department of Bioengineering, 501 Rhodes Engineering Research Center, Clemson University, Clemson, South Carolina, 29634.
Robert A
RA
Latour
D000465:Algorithms; D016000:Cluster Analysis; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
D011506:Proteins
Cluster analysis; conformation; molecular dynamics; orientation; protein adsorption