title: deltaGseg: macrostate estimation via molecular dynamics simulations and multiscale time series analysis.
abstract: CONCLUSIONS
  Binding free energy calculations obtained through molecular dynamics simulations reflect intermolecular interaction states through a series of independent snapshots. Typically, the free energies of multiple simulated series (each with slightly different starting conditions) need to be estimated. Previous approaches carry out this task by moving averages at certain decorrelation times, assuming that the system comes from a single conformation description of binding events. Here, we discuss a more general approach that uses statistical modeling, wavelets denoising and hierarchical clustering to estimate the significance of multiple statistically distinct subpopulations, reflecting potential macrostates of the system. We present the deltaGseg R package that performs macrostate estimation from multiple replicated series and allows molecular biologists/chemists to gain physical insight into the molecular details that are not easily accessible by experimental techniques.
  
  
  BACKGROUND
  deltaGseg is a Bioconductor R package available at http://bioconductor.org/packages/release/bioc/html/deltaGseg.html.
authors.affiliation: Institute of Molecular and Cell Biology, Epigenetics, Chromatin and Differentiation, 61 Biopolis Street, Proteos #03-06, Singapore 138673 and Bioinformatics Institute, Genome and Gene Expression Data Analysis, 30 Biopolis Street, Matrix #07-01, Singapore 138671.
authors.forename: Diana H P
authors.initials: DH
authors.lastname: Low
authors.forename: Efthymios
authors.initials: E
authors.lastname: Motakis
mesh_terms: D016000:Cluster Analysis; D006801:Humans; D056004:Molecular Dynamics Simulation; D012984:Software