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Molecular docking performance evaluated on the D3R Grand Challenge 2015 drug-like ligand datasets

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Abstract

The D3R Grand Challenge 2015 was focused on two protein targets: Heat Shock Protein 90 (HSP90) and Mitogen-Activated Protein Kinase Kinase Kinase Kinase 4 (MAP4K4). We used a protocol involving a preliminary analysis of the available data in PDB and PubChem BioAssay, and then a docking/scoring step using more computationally demanding parameters that were required to provide more reliable predictions. We could evidence that different docking software and scoring functions can behave differently on individual ligand datasets, and that the flexibility of specific binding site residues is a crucial element to provide good predictions.

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Acknowledgments

Fellowships from the LabEx LERMIT (E.S.) and the ERC Advanced Grant OSAI (V. M.) are gratefully acknowledged. B. I. I.’s laboratory is member of the Laboratory of Excellence in Research on Medication and Innovative Therapeutics (LabEx LERMIT), supported by a Grant from French National Research Agency (ANR-10-LABX-33). We would like to thank the D3R Grand Challenge 2015 organizers for their help throughout the submission and evaluation process.

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Authors and Affiliations

  1. Institut de Chimie des Substances Naturelles, CNRS UPR 2301, LabEx LERMIT, Université Paris-Saclay, 91198, Gif-sur-Yvette, France

    Edithe Selwa, Virginie Y. Martiny & Bogdan I. Iorga

  2. Department of Nephrology and Dialysis, AP-HP, Tenon Hospital, INSERM UMR-S 1155, 75020, Paris, France

    Virginie Y. Martiny

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  1. Edithe Selwa
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Correspondence to Bogdan I. Iorga.

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Selwa, E., Martiny, V.Y. & Iorga, B.I. Molecular docking performance evaluated on the D3R Grand Challenge 2015 drug-like ligand datasets. J Comput Aided Mol Des 30, 829–839 (2016). https://doi.org/10.1007/s10822-016-9983-3

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