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A consistent description of HYdrogen bond and DEhydration energies in protein–ligand complexes: methods behind the HYDE scoring function

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Abstract

The estimation of free energy of binding is a key problem in structure-based design. We developed the scoring function HYDE based on a consistent description of HYdrogen bond and DEhydration energies in protein–ligand complexes. HYDE is applicable to all types of protein targets since it is not calibrated on experimental binding affinity data or protein–ligand complexes. The comprehensible atom-based score of HYDE is visualized by applying a very intuitive coloring scheme, thereby facilitating the analysis of protein–ligand complexes in the lead optimization process. In this paper, we have revised several aspects of the former version of HYDE which was described in detail previously. The revised HYDE version was already validated in large-scale redocking and screening experiments which were performed in the course of the Docking and Scoring Symposium at 241st ACS National Meeting. In this study, we additionally evaluate the ability of the revised HYDE version to predict binding affinities. On the PDBbind 2007 coreset, HYDE achieves a correlation coefficient of 0.62 between the experimental binding constants and the predicted binding energy, performing second best on this dataset compared to 17 other well-established scoring functions. Further, we show that the performance of HYDE in large-scale redocking and virtual screening experiments on the Astex diverse set and the DUD dataset respectively, is comparable to the best methods in this field.

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Acknowledgments

The authors want to thank Hans Briem and Kristin Beyer of Bayer Pharma AG and Jürgen Albrecht of Bayer CropScience AG for many fruitful discussions and a successful cooperation. We also thank Holger Claussen, Marcus Gastreich and Christian Lemmen of BioSolveIT GmbH for their on-going support during the development of HYDE, particularly for the meticulous testing and analysis of HYDE and resulting valuable feedback. The HYDE project was funded by Bayer CropScience AG and Bayer Pharma AG.

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Authors and Affiliations

  1. Center for Bioinformatics, University of Hamburg, Bundesstr. 43, 20146, Hamburg, Germany

    Nadine Schneider & Matthias Rarey

  2. Bayer CropScience AG, Industriepark Hoechst, G836, 65926, Frankfurt am Main, Germany

    Gudrun Lange & Robert Klein

  3. BioSolveIT GmbH, An Der Ziegelei 79, 53757, St. Augustin, Germany

    Sally Hindle

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  1. Nadine Schneider
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  5. Matthias Rarey
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Correspondence to Matthias Rarey.

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Schneider, N., Lange, G., Hindle, S. et al. A consistent description of HYdrogen bond and DEhydration energies in protein–ligand complexes: methods behind the HYDE scoring function. J Comput Aided Mol Des 27, 15–29 (2013). https://doi.org/10.1007/s10822-012-9626-2

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