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GalaxyDock BP2 score: a hybrid scoring function for accurate protein–ligand docking

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Abstract

Protein–ligand docking is a useful tool for providing atomic-level understanding of protein functions in nature and design principles for artificial ligands or proteins with desired properties. The ability to identify the true binding pose of a ligand to a target protein among numerous possible candidate poses is an essential requirement for successful protein–ligand docking. Many previously developed docking scoring functions were trained to reproduce experimental binding affinities and were also used for scoring binding poses. However, in this study, we developed a new docking scoring function, called GalaxyDock BP2 Score, by directly training the scoring power of binding poses. This function is a hybrid of physics-based, empirical, and knowledge-based score terms that are balanced to strengthen the advantages of each component. The performance of the new scoring function exhibits significant improvement over existing scoring functions in decoy pose discrimination tests. In addition, when the score is used with the GalaxyDock2 protein–ligand docking program, it outperformed other state-of-the-art docking programs in docking tests on the Astex diverse set, the Cross2009 benchmark set, and the Astex non-native set. GalaxyDock BP2 Score and GalaxyDock2 with this score are freely available at http://galaxy.seoklab.org/softwares/galaxydock.html.

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Acknowledgements

This work was supported by the National Research Foundation of Korea (NRF) grants funded by the Ministry of Science, ICT & Future Planning (Nos. 2016R1A2A1A05005485 and 2016M3C4A7952630) and by the Korea Institute of Science and Technology Information supercomputing center (KSC-2015-C2-057). We thank Andrew Beaven for his careful reading of the manuscript.

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  1. Woong-Hee Shin

    Present address: Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA

Authors and Affiliations

  1. Department of Chemistry, Seoul National University, Seoul, Republic of Korea

    Minkyung Baek, Woong-Hee Shin & Chaok Seok

  2. Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea

    Hwan Won Chung & Chaok Seok

  3. Computational Science Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea

    Hwan Won Chung

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Correspondence to Chaok Seok.

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Baek, M., Shin, WH., Chung, H.W. et al. GalaxyDock BP2 score: a hybrid scoring function for accurate protein–ligand docking. J Comput Aided Mol Des 31, 653–666 (2017). https://doi.org/10.1007/s10822-017-0030-9

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