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ORAL PRESENTATION Open Access
Use of DEKOIS 2.0 to gain insights for virtualscreeningFrank M Boeckler*, Matthias R Bauer, Tamer M Ibrahim, Simon M Vogel
From 9th German Conference on ChemoinformaticsFulda, Germany. 10-12 November 2013
With DEKOIS we have created an automated workflowto efficiently generate decoy sets based on a certain num-ber of actives for any target [1]. Physico-chemical similar-ity should be maximized between decoys and actives inorder to yield challenging sets for benchmarking, whileexact mimicking of potentially active substructuresshould be avoided to omit latent actives in the decoy set(LADS). Overall, the diversity of actives and decoysshould be maximized to avoid artifacts based on clusters.Applying this philosophy, we have added more details todescribe the physicochemical space and applied this pro-tocol to generate sets for targets which had not beenaccessible before. These DEKOIS 2.0 sets [2] are availableonline (http://www.dekois.com) for benchmarking anddevelopment of new tailor-made scoring functions.Further extension toward additional targets can facilitatea systematic comparison of the virtual screening perfor-mance of docking tools and scoring functions in a targetdependent way. Based on DEKOIS 2.0, we have investi-gated strengths and weaknesses of popular docking toolsand scoring functions. In addition, we assessed how dif-ferences in the setup and preparation can affect thepROC profiles and early enrichment, in particular [3].For this analysis we have developed an automated proto-col to identify and highlight chemotype-specific differ-ences in ligand recognition.
Published: 11 March 2014
References1. Vogel SM, Bauer MR, Boeckler FM: DEKOIS: demanding evaluation kits for
objective in silico screening–a versatile tool for benchmarking dockingprograms and scoring functions. J Chem Inf Model 2011, 51:2650-2665.
2. Bauer MR, Ibrahim TM, Vogel SM, Boeckler FM: Evaluation andOptimization of Virtual Screening Workflows with DEKOIS 2.0 – A Public
Library of Challenging Docking Benchmark Sets. J Chem Inf Model 2013,53:1447-1462.
3. Ibrahim TM, Bauer MR, Vogel SM, Boeckler FM:, , in preparation.
doi:10.1186/1758-2946-6-S1-O24Cite this article as: Boeckler et al.: Use of DEKOIS 2.0 to gain insights forvirtual screening. Journal of Cheminformatics 2014 6(Suppl 1):O24.
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* Correspondence: [email protected] of Pharmacy & Biochemistry, Eberhard Karls University,Tuebingen, 72076, Germany
Boeckler et al. Journal of Cheminformatics 2014, 6(Suppl 1):O24http://www.jcheminf.com/content/6/S1/O24
© 2014 Boeckler et al; licensee Chemistry Central Ltd. This is an Open Access article distributed under the terms of the CreativeCommons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, andreproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
