Development of a method to discover high affinity ligands using molecular dynamics simulation

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The free energy perturbation (FEP)/Thermodynamic integration (TI) methods were applied to explore high affinity ligands with a small structural change to a known ligand. By changing various calculation conditions, affinity differences among protein kinase CK2 ligands could be reproduced with high accuracy. Possibly novel potent ligands for CK2 protein were discovered by exhaustive prediction of synthetic feasible ligands. The optimized calculation condition gives good reproducibility and this prediction method is useful in drug discovery.