Binding estimation after refinement (BEAR) is a novel automated computational procedure suitable for correcting and overcoming limitations of docking procedures such as poor scoring function and the generation of unreasonable ligand conformations. BEAR makes use of molecular dynamics simulation followed by MM-PBSA and MM-GBSA binding free energy estimates as tools to refine and rescore the structures obtained from docking virtual screenings. As binding estimation after refinement relies on molecular dynamics, the entire procedure can be tailored to the needs of the end-user in terms of computational time and the desired accuracy of the results. In a validation test, binding estimation after refinement and rescoring resulted in a significant enrichment of known ligands among top scoring compounds compared with the original docking results. Binding estimation after refinement has direct and straightforward application in virtual screening for correcting both false-positive and false-negative hits, and should facilitate more reliable selection of biologically active molecules from compound databases.