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J Chem Inf Model. 2011 Nov 28;51(11):2994-3004. doi: 10.1021/ci2003939. Epub 2011 Oct 28.

Knowledge-based scoring functions in drug design: 3. A two-dimensional knowledge-based hydrogen-bonding potential for the prediction of protein-ligand interactions.

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  • 1Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.


Hydrogen bonding is a key contributor to the molecular recognition between ligands and their host molecules in biological systems. Here we develop a novel orientation-dependent hydrogen bonding potential based on the geometric characteristics of hydrogen bonds observed in 44,585 protein-ligand complexes. We find a close correspondence between the empirical knowledge and the energy landscape inferred from the distribution of HBs. A scoring function based on the resultant hydrogen-bonding potentials discriminates native protein-ligand structures from incorrectly docked decoys with remarkable predictive power.

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