title: Automated crystallographic ligand building using the medial axis transform of an electron-density isosurface.
abstract: Automatic fitting methods that build molecules into electron-density maps usually fail below 3.5 A resolution. As a first step towards addressing this problem, an algorithm has been developed using an approximation of the medial axis to simplify an electron-density isosurface. This approximation captures the central axis of the isosurface with a graph which is then matched against a graph of the molecular model. One of the first applications of the medial axis to X-ray crystallography is presented here. When applied to ligand fitting, the method performs at least as well as methods based on selecting peaks in electron-density maps. Generalization of the method to recognition of common features across multiple contour levels could lead to powerful automatic fitting methods that perform well even at low resolution.
authors.affiliation: Department of Molecular and Cellular Physiology, Stanford Synchrotron Radiation Laboratory, Stanford, CA, USA.
authors.forename: Jun
authors.initials: J
authors.lastname: Aishima
authors.forename: Daniel S
authors.initials: DS
authors.lastname: Russel
authors.forename: Leonidas J
authors.initials: LJ
authors.lastname: Guibas
authors.forename: Paul D
authors.initials: PD
authors.lastname: Adams
authors.forename: Axel T
authors.initials: AT
authors.lastname: Brunger
mesh_terms: D000465:Algorithms; D001331:Automation; D018360:Crystallography, X-Ray / Q000379:methods*; D004583:Electrons; D008024:Ligands; D046911:Macromolecular Substances / Q000737:chemistry*; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D010363:Pattern Recognition, Automated; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry
chemical_list: D008024:Ligands; D046911:Macromolecular Substances; D011506:Proteins