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Evaluation of docking performance in a blinded virtual screening of fragment-like trypsin inhibitors

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Abstract

In this study, we have “blindly” assessed the ability of several combinations of docking software and scoring functions to predict the binding of a fragment-like library of bovine trypsine inhibitors. The most suitable protocols (involving Gold software and GoldScore scoring function, with or without rescoring) were selected for this purpose using a training set of compounds with known biological activities. The selected virtual screening protocols provided good results with the SAMPL3-VS dataset, showing enrichment factors of about 10 for Top 20 compounds. This methodology should be useful in difficult cases of docking, with a special emphasis on the fragment-based virtual screening campaigns.

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Abbreviations

RMSD:

Root mean square deviation

ROC:

Receiver operating characteristic

AUC:

Area under curve

CI:

Confidence interval

QPLD:

QM-Polarized ligand docking

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Authors and Affiliations

  1. Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Centre de Recherche de Gif-sur-Yvette, Avenue de la Terrasse, 91198, Gif-sur-Yvette, France

    Georgiana Surpateanu & Bogdan I. Iorga

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  1. Georgiana Surpateanu
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  2. Bogdan I. Iorga
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Correspondence to Bogdan I. Iorga.

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Surpateanu, G., Iorga, B.I. Evaluation of docking performance in a blinded virtual screening of fragment-like trypsin inhibitors. J Comput Aided Mol Des 26, 595–601 (2012). https://doi.org/10.1007/s10822-011-9526-x

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  • DOI: https://doi.org/10.1007/s10822-011-9526-x

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