Modelling bound ligands in protein crystal structures

P. H. Zwart, G. G. Langer, V. S. Lamzin
2004 Acta Crystallographica Section D: Biological Crystallography  
Methods for automated identi®cation and building of proteinbound ligands in electron-density maps are described. An error model of the geometrical features of the molecular structure of a ligand based on a lattice distribution of positional parameters is obtained via simulation and is used for the construction of an approximate likelihood scoring function. This scoring function combined with a graph-based search technique provides a¯exible model-building scheme and its application shows
more » ... g initial results. Several ligands with sizes ranging from 9 to 44 non-H atoms have been identi®ed in various X-ray structures and built in an automatic way using a minimal amount of prior stereochemical knowledge.
doi:10.1107/s0907444904012995 pmid:15572776 fatcat:jbmru5jicberxo3cnw2ppjftfu