title: On the functional significance of electron density protein structure alignments.
abstract: Electron density protein alignments are analyzed in terms of their underlying similarity measure, the density overlap. These alignments are conceptually unrelated to biochemical structural elements and, therefore, are appropriate in structure-only similarity studies. The analysis is focused on the low sequence similarity subset of protein domains. A remarkable association is found between simple, density overlap measures and the expert designed Structural Classification of Proteins (SCOP) for which functional and evolutive analogies prevail. The association found validates the functional significance of electron density alignments.
authors.affiliation: Department of Chemistry, Rice University, Houston, Texas, USA. constans@ruf.rice.edu
authors.forename: Pere
authors.initials: P
authors.lastname: Constans
mesh_terms: D016000:Cluster Analysis; D003627:Data Interpretation, Statistical; D004583:Electrons; D008958:Models, Molecular; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000502:physiology; D011789:Quantum Theory; D040681:Structural Homology, Protein
chemical_list: D011506:Proteins