title: EvDTree: structure-dependent substitution profiles based on decision tree classification of 3D environments.
abstract: BACKGROUND
  Structure-dependent substitution matrices increase the accuracy of sequence alignments when the 3D structure of one sequence is known, and are successful e.g. in fold recognition. We propose a new automated method, EvDTree, based on a decision tree algorithm, for automatic derivation of amino acid substitution probabilities from a set of sequence-structure alignments. The main advantage over other approaches is an unbiased automatic selection of the most informative structural descriptors and associated values or thresholds. This feature allows automatic derivation of structure-dependent substitution scores for any specific set of structures, without the need to empirically determine best descriptors and parameters.
  
  
  RESULTS
  Decision trees for residue substitutions were constructed for each residue type from sequence-structure alignments extracted from the HOMSTRAD database. For each tree cluster, environment-dependent substitution profiles were derived. The resulting structure-dependent substitution scores were assessed using a criterion based on the mean ranking of observed substitution among all possible substitutions and in sequence-structure alignments. The automatically built EvDTree substitution scores provide significantly better results than conventional matrices and similar or slightly better results than other structure-dependent matrices. EvDTree has been applied to small disulfide-rich proteins as a test case to automatically derive specific substitutions scores providing better results than non-specific substitution scores. Analyses of the decision tree classifications provide useful information on the relative importance of different structural descriptors.
  
  
  CONCLUSIONS
  We propose a fully automatic method for the classification of structural environments and inference of structure-dependent substitution profiles. We show that this approach is more accurate than existing methods for various applications. The easy adaptation of EvDTree to any specific data set opens the way for class-specific structure-dependent substitution scores which can be used in threading-based remote homology searches.
authors.affiliation: Centre de Biochimie Structurale, Faculté de Pharmacie, Université Montpellier I, 15 avenue Charles Flahault, 34093 Montpellier Cedex 5, France. gelly@cbs.cnrs.fr <gelly@cbs.cnrs.fr>
authors.forename: Jean-Christophe
authors.initials: JC
authors.lastname: Gelly
authors.forename: Laurent
authors.initials: L
authors.lastname: Chiche
authors.forename: Jérôme
authors.initials: J
authors.lastname: Gracy
mesh_terms: D000409:Alanine / Q000737:chemistry; D000465:Algorithms; D001331:Automation; D016000:Cluster Analysis; D019295:Computational Biology / Q000295:instrumentation* / Q000379:methods*; D003198:Computer Simulation; D003628:Database Management Systems; D030562:Databases, Protein; D003663:Decision Trees; D004220:Disulfides; D019143:Evolution, Molecular; D006801:Humans; D016247:Information Storage and Retrieval; D015233:Models, Statistical; D008969:Molecular Sequence Data; D016017:Odds Ratio; D017433:Protein Structure, Secondary; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D004220:Disulfides; D000409:Alanine