This paper describes the construction, validation and application of an act
ive site model of the serine protease thrombin. Initial use was made of med
ium resolution X-ray crystallographic structures of thrombin complexed with
low molecular weight, non-specific inhibitors to create a computationally
useable active site shell of the enzyme. Molecular mechanics methods were t
hen applied to dock known ligands into the active site region in order to d
erive a model that would accurately predict binding conformations. Validati
on of the modelling process was achieved by comparison of the predicted enz
yme-bound conformations with their known, crystallographic binding conforma
tions. The resultant model was used extensively for predictive purposes pri
or to obtaining confirmatory crystal data relating to a ligand possessing a
novel and unexpected binding component complexed to thrombin. The data ser
ved both to confirm the accuracy of the binding site model and to provide i
nformation for the further refinement of the model.