title: A dissimilarity matrix between protein atom classes based on Gaussian mixtures.
abstract: BACKGROUND
  Previously, Rantanen et al. (2001; J. Mol. Biol., 313, 197-214) constructed a protein atom-ligand fragment interaction library embodying experimentally solved, high-resolution three-dimensional (3D) structural data from the Protein Data Bank (PDB). The spatial locations of protein atoms that surround ligand fragments were modeled with Gaussian mixture models, the parameters of which were estimated with the expectation-maximization (EM) algorithm. In the validation analysis of this library, there was strong indication that the protein atom classification, 24 classes, was too large and that a reduction in the classes would lead to improved predictions.
  
  
  RESULTS
  Here, a dissimilarity (distance) matrix that is suitable for comparison and fusion of 24 pre-defined protein atom classes has been derived. Jeffreys' distances between Gaussian mixture models are used as a basis to estimate dissimilarities between protein atom classes. The dissimilarity data are analyzed both with a hierarchical clustering method and independently by using multidimensional scaling analysis. The results provide additional insight into the relationships between different protein atom classes, giving us guidance on, for example, how to readjust protein atom classification and, thus, they will help us to improve protein--ligand interaction predictions.
  
  
  BACKGROUND
  vira@utu.fi
authors.affiliation: Department of Mathematics, University of Turku, FIN-20014 Turku, Finland.
authors.forename: Ville-Veikko
authors.initials: VV
authors.lastname: Rantanen
authors.forename: Mats
authors.initials: M
authors.lastname: Gyllenberg
authors.forename: Timo
authors.initials: T
authors.lastname: Koski
authors.forename: Mark S
authors.initials: MS
authors.lastname: Johnson
mesh_terms: D016000:Cluster Analysis; D030562:Databases, Protein; D008024:Ligands; D008958:Models, Molecular; D015233:Models, Statistical; D016011:Normal Distribution; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000145:classification*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity
chemical_list: D008024:Ligands; D011506:Proteins