Cart
Article
Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms
Full Text HTML
Hi-Res PDFPurchase the full-text
- PDF/HTML,
figures/images,
references and tables,
(where available)
Section:Abstract
Molecular dynamics simulation methods produce trajectories of atomic positions (and optionally velocities and energies) as a function of time and provide a representation of the sampling of a given molecule's energetically accessible conformational ensemble. As simulations on the 10−100 ns time scale become routine, with sampled configurations stored on the picosecond time scale, such trajectories contain large amounts of data. Data-mining techniques, like clustering, provide one means to group and make sense of the information in the trajectory. In this work, several clustering algorithms were implemented, compared, and utilized to understand MD trajectory data. The development of the algorithms into a freely available C code library, and their application to a simple test example of random (or systematically placed) points in a 2D plane (where the pairwise metric is the distance between points) provide a means to understand the relative performance. Eleven different clustering algorithms were developed, ranging from top-down splitting (hierarchical) and bottom-up aggregating (including single-linkage edge joining, centroid-linkage, average-linkage, complete-linkage, centripetal, and centripetal-complete) to various refinement (means, Bayesian, and self-organizing maps) and tree (COBWEB) algorithms. Systematic testing in the context of MD simulation of various DNA systems (including DNA single strands and the interaction of a minor groove binding drug DB226 with a DNA hairpin) allows a more direct assessment of the relative merits of the distinct clustering algorithms. Additionally, means to assess the relative performance and differences between the algorithms, to dynamically select the initial cluster count, and to achieve faster data mining by “sieved clustering” were evaluated. Overall, it was found that there is no one perfect “one size fits all” algorithm for clustering MD trajectories and that the results strongly depend on the choice of atoms for the pairwise comparison. Some algorithms tend to produce homogeneously sized clusters, whereas others have a tendency to produce singleton clusters. Issues related to the choice of a pairwise metric, clustering metrics, which atom selection is used for the comparison, and about the relative performance are discussed. Overall, the best performance was observed with the average-linkage, means, and SOM algorithms. If the cluster count is not known in advance, the hierarchical or average-linkage clustering algorithms are recommended. Although these algorithms perform well, it is important to be aware of the limitations or weaknesses of each algorithm, specifically the high sensitivity to outliers with hierarchical, the tendency to generate homogenously sized clusters with means, and the tendency to produce small or singleton clusters with average-linkage.
Citing Articles
Citation data is made available by participants in CrossRef's Cited-by Linking service. For a more comprehensive list of citations to this article, users are encouraged to perform a search in SciFinder.
This article has been cited by 29 ACS Journal articles (5 most recent appear below).
Efficient Construction of Mesostate Networks from Molecular Dynamics Trajectories
Andreas Vitalis and Amedeo CaflischJournal of Chemical Theory and Computation2012 Article ASAPEfficient Construction of Mesostate Networks from Molecular Dynamics Trajectories
Andreas Vitalis and Amedeo CaflischJournal of Chemical Theory and Computation2012 Article ASAPThe coarse-graining of data from molecular simulations yields conformational space networks that may be used for predicting the system’s long time scale behavior, to discover structural pathways connecting free energy basins in the system, or simply to ...
The Structural Role of Mg2+ Ions in a Class I RNA Polymerase Ribozyme: A Molecular Simulation Study
Jacopo Sgrignani and Alessandra MagistratoThe Journal of Physical Chemistry B2012 Article ASAPThe Structural Role of Mg2+ Ions in a Class I RNA Polymerase Ribozyme: A Molecular Simulation Study
Jacopo Sgrignani and Alessandra MagistratoThe Journal of Physical Chemistry B2012 Article ASAPAccording to the RNA world hypothesis, self-replicating ribozymes, storing the genetic information and being able to perform catalysis, were the constituents of the first living organisms. In particular, RNA polymerase ribozymes, similar to current ...
The Carbohydrate-Binding Site in Galectin-3 Is Preorganized To Recognize a Sugarlike Framework of Oxygens: Ultra-High-Resolution Structures and Water Dynamics
Kadhirvel Saraboji, Maria Håkansson, Samuel Genheden, Carl Diehl, Johan Qvist, Ulrich Weininger, Ulf J. Nilsson, Hakon Leffler, Ulf Ryde, Mikael Akke, and Derek T. LoganBiochemistry2012 51 (1), 296-306The Carbohydrate-Binding Site in Galectin-3 Is Preorganized To Recognize a Sugarlike Framework of Oxygens: Ultra-High-Resolution Structures and Water Dynamics
Kadhirvel Saraboji, Maria Håkansson, Samuel Genheden, Carl Diehl, Johan Qvist, Ulrich Weininger, Ulf J. Nilsson, Hakon Leffler, Ulf Ryde, Mikael Akke, and Derek T. LoganBiochemistry2012 51 (1), 296-306The recognition of carbohydrates by proteins is a fundamental aspect of communication within and between living cells. Understanding the molecular basis of carbohydrate–protein interactions is a prerequisite for the rational design of synthetic ligands. ...
Simulations of Allosteric Motions in the Zinc Sensor CzrA
Dhruva K. Chakravorty, Bing Wang, Chul Won Lee, David P. Giedroc, and Kenneth M. Merz, Jr.Journal of the American Chemical Society2011 Article ASAPSimulations of Allosteric Motions in the Zinc Sensor CzrA
Dhruva K. Chakravorty, Bing Wang, Chul Won Lee, David P. Giedroc, and Kenneth M. Merz, Jr.Journal of the American Chemical Society2011 Article ASAPThe zinc sensing transcriptional repressor Staphylococcus aureus CzrA represents an excellent model system to understand how metal sensor proteins maintain cellular metal homeostasis. Zn(II) binding induces a quaternary structural switch from a “closed” ...
Base- and Structure-Dependent DNA Dinucleotide–Carbon Nanotube Interactions: Molecular Dynamics Simulations and Thermodynamic Analysis
Zhengtao Xiao, Xia Wang, Xue Xu, Hong Zhang, Yan Li, and Yonghua WangThe Journal of Physical Chemistry C2011 115 (44), 21546-21558Base- and Structure-Dependent DNA Dinucleotide–Carbon Nanotube Interactions: Molecular Dynamics Simulations and Thermodynamic Analysis
Zhengtao Xiao, Xia Wang, Xue Xu, Hong Zhang, Yan Li, and Yonghua WangThe Journal of Physical Chemistry C2011 115 (44), 21546-21558Wrapping of single-wall carbon nanotubes (SWCNTs) by single-stranded DNA (ssDNA) was found to be sequence-dependent, offering properties such as the facilitation of SWCN sorting, ultrafast DNA sequencing, and construction of chemical sensors. Although the ...
Tools
-
Add to Favorites
-
Download Citation
-
Email a Colleague -
Permalink
Order Reprints
Rights & Permissions
Citation Alerts
Accession Codes
History
- Published In Issue November 13, 2007
- Received May 17, 2007
ACS
Network
Facebook
Tweet This
CiteULike
Newsvine
Digg This
Delicious
