Modelling bound ligands in protein crystal structures.
Methods for automated identification and building of protein-bound 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 flexible model-building scheme and its application shows promising initial results. Several ligands with sizes ranging from 9 to 44 non-H atoms have been identified in various X-ray structures and built in an automatic way using a minimal amount of prior stereochemical knowledge.
Zwart
P H
PH
European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, Building 25A, 22603 Hamburg, Germany.
Langer
G G
GG
Lamzin
V S
VS
D000249:Adenosine Monophosphate / Q000737:chemistry; D000255:Adenosine Triphosphate / Q000737:chemistry; D000465:Algorithms; D001550:Benzamidines / Q000737:chemistry; D019826:Cholic Acid / Q000737:chemistry; D018360:Crystallography, X-Ray; D004099:Dihydroxyacetone Phosphate / Q000737:chemistry; D004583:Electrons; D006860:Hydrogen Bonding; D008024:Ligands; D008958:Models, Molecular; D009243:NAD / Q000737:chemistry; D011374:Progesterone / Q000737:chemistry; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D014212:Tretinoin / Q000737:chemistry
D001550:Benzamidines; D008024:Ligands; D011506:Proteins; D009243:NAD; D000249:Adenosine Monophosphate; D011374:Progesterone; D014212:Tretinoin; D004099:Dihydroxyacetone Phosphate; D000255:Adenosine Triphosphate; D019826:Cholic Acid; C005555:propamidine