Journal of Computer-Aided Molecular Design

, Volume 26, Issue 5, pp 595–601 | Cite as

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

Article

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.

Keywords

Virtual screening Docking Scoring function Fragment-like compounds Trypsin inhibitors 

Abbreviations

RMSD

Root mean square deviation

ROC

Receiver operating characteristic

AUC

Area under curve

CI

Confidence interval

QPLD

QM-Polarized ligand docking

Supplementary material

10822_2011_9526_MOESM1_ESM.pdf (229 kb)
Supplementary material 1 (PDF 229 kb)

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Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  1. 1.Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Centre de Recherche de Gif-sur-YvetteGif-sur-YvetteFrance

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