Automated crystallographic ligand building using the medial axis transform of an electron-density isosurface.
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.
Aishima
Jun
J
Department of Molecular and Cellular Physiology, Stanford Synchrotron Radiation Laboratory, Stanford, CA, USA.
Russel
Daniel S
DS
Guibas
Leonidas J
LJ
Adams
Paul D
PD
Brunger
Axel T
AT
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
D008024:Ligands; D046911:Macromolecular Substances; D011506:Proteins