ArticleJournal of computer-aided molecular design2014
Virtual screening of the SAMPL4 blinded HIV integrase inhibitors dataset.
Article in Journal of computer-aided molecular design, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
5 citing papers in PubMed.
- Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset.Journal of computer-aided molecular design · 2019Article
- Blinded evaluation of cathepsin S inhibitors from the D3RGC3 dataset using molecular docking and free energy calculations.Journal of computer-aided molecular design · 2019Article
- Blinded evaluation of farnesoid X receptor (FXR) ligands binding using molecular docking and free energy calculations.Journal of computer-aided molecular design · 2018Article
- Herb-target interaction network analysis helps to disclose molecular mechanism of traditional Chinese medicine.Scientific reports · 2016Article
- Molecular docking performance evaluated on the D3R Grand Challenge 2015 drug-like ligand datasets.Journal of computer-aided molecular design · 2016Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Several combinations of docking software and scoring functions were evaluated for their ability to predict the binding of a dataset of potential HIV integrase inhibitors. We found that different docking software were appropriate for each one of the three binding sites considered (LEDGF, Y3 and fragment sites), and the most suitable two docking protocols, involving Glide SP and Gold ChemScore, were selected using a training set of compounds identified from the structural data available. These protocols could successfully predict respectively 20.0 and 23.6 % of the HIV integrase binders, all of them being present in the LEDGF site. When a different analysis of the results was carried out by removing all alternate isomers of binders from the set, our predictions were dramatically improved, with an overall ROC AUC of 0.73 and enrichment factor at 10 % of 2.89 for the prediction obtained using Gold ChemScore. This study highlighted the ability of the selected docking protocols to correctly position in most cases the ortho-alkoxy-carboxylate core functional group of the ligands in the corresponding binding site, but also their difficulties to correctly rank the docking poses.
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Registered trials
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