HYDE1,2 is a novel, atom-based scoring function which is based on HYdration and DEsolvation terms. It reflects the Gibbs free energy of binding while only considering the essential interactions of protein-ligand complexes.The intuitive atom-based score allows the direct visualization of favorable and unfavorable ligand modifications during the lead optimization process. This supports the medicinal chemists in understanding protein-ligand interactions and designing new bioactive compounds. We show how to use HYDE for SAR analysis in different congeneric compound series.Since the first presentation of HYDE, the function has been applied in several different scenarios and on many different proteins. Using the Astex diverse set, HYDE successfully predicts the correct binding mode in 93% of the complexes. In addition, using the DUD and the WOMBAT dataset, HYDE shows significant enrichment values in virtual screening. Furthermore, we show the application of HYDE in the analysis of protein-protein interactions3.  References:1.  R. Reulecke, G. Lange, R. Klein, J. Albrecht, M. Rarey, ChemMedChem 2008 , 3, 885 � 8972.  N. Schneider, S. Hindle, G. Lange, R. Klein, J. Albrecht, H. Briem, K. Beyer, H. Claussen,        M. Gastreich, C. Lemmen, M. Rarey, J. Comp. Aided Mol. Des. 2011 , submitted3.  E. Vennmann, N. Schneider, G. Lange, M. Rarey, 2011 , submitted

HYDE in practice: Understanding protein-ligand interactions

243rd National Meeting (2012)

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