Use of DEKOIS 2.0 to gain insights for virtual screening
© Boeckler et al; licensee Chemistry Central Ltd. 2014
Published: 11 March 2014
With DEKOIS we have created an automated workflow to efficiently generate decoy sets based on a certain number of actives for any target . Physico-chemical similarity should be maximized between decoys and actives in order to yield challenging sets for benchmarking, while exact mimicking of potentially active substructures should be avoided to omit latent actives in the decoy set (LADS). Overall, the diversity of actives and decoys should be maximized to avoid artifacts based on clusters. Applying this philosophy, we have added more details to describe the physicochemical space and applied this protocol to generate sets for targets which had not been accessible before. These DEKOIS 2.0 sets  are available online (http://www.dekois.com) for benchmarking and development of new tailor-made scoring functions. Further extension toward additional targets can facilitate a systematic comparison of the virtual screening performance of docking tools and scoring functions in a target dependent way. Based on DEKOIS 2.0, we have investigated strengths and weaknesses of popular docking tools and scoring functions. In addition, we assessed how differences in the setup and preparation can affect the pROC profiles and early enrichment, in particular . For this analysis we have developed an automated protocol to identify and highlight chemotype-specific differences in ligand recognition.
- Vogel SM, Bauer MR, Boeckler FM: DEKOIS: demanding evaluation kits for objective in silico screening--a versatile tool for benchmarking docking programs and scoring functions. J Chem Inf Model. 2011, 51: 2650-2665. 10.1021/ci2001549.View ArticleGoogle Scholar
- Bauer MR, Ibrahim TM, Vogel SM, Boeckler FM: Evaluation and Optimization of Virtual Screening Workflows with DEKOIS 2.0 – A Public Library of Challenging Docking Benchmark Sets. J Chem Inf Model. 2013, 53: 1447-1462. 10.1021/ci400115b.View ArticleGoogle Scholar
- Ibrahim TM, Bauer MR, Vogel SM, Boeckler FM: , in preparationGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction 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.