Impact of ligand protonation on virtual screening against β-secretase (BACE1)

Structure-based virtual screens were carried out against β-secretase (BACE1) to investigate the impact of ligand protonation on screening efficacy. A comparative evaluation of the performance and its dependence on ligand protonation states docking by Surflex, eHiTS, GOLD, and FlexX-Pharm was performed. Virtual screening performed by FlexX-Pharm (EF(1%)=69) and Surflex (EF(1%)=58) provided the best efficiency. Screening protocols by FlexX-Pharm and GOLD were affected by ligand protonation, while performance of Surflex did not depend on ligand protonation.


Tímea Polgár, Csaba Magyar, István Simon, György M. Keserü
November 1, 2007
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