Mining Chemical Activity Status from High-Throughput Screening Assays
Ba Alawi, Wail
Afeef, Moataz A.
Bajic, Vladimir B.
KAUST DepartmentComputational Bioscience Research Center (CBRC)
KAUST Catalysis Center (KCC)
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Computer Science Program
Chemical Science Program
Physical Sciences and Engineering (PSE) Division
Applied Mathematics and Computational Science Program
Permanent link to this recordhttp://hdl.handle.net/10754/596363
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AbstractHigh-throughput screening (HTS) experiments provide a valuable resource that reports biological activity of numerous chemical compounds relative to their molecular targets. Building computational models that accurately predict such activity status (active vs. inactive) in specific assays is a challenging task given the large volume of data and frequently small proportion of active compounds relative to the inactive ones. We developed a method, DRAMOTE, to predict activity status of chemical compounds in HTP activity assays. For a class of HTP assays, our method achieves considerably better results than the current state-of-the-art-solutions. We achieved this by modification of a minority oversampling technique. To demonstrate that DRAMOTE is performing better than the other methods, we performed a comprehensive comparison analysis with several other methods and evaluated them on data from 11 PubChem assays through 1,350 experiments that involved approximately 500,000 interactions between chemicals and their target proteins. As an example of potential use, we applied DRAMOTE to develop robust models for predicting FDA approved drugs that have high probability to interact with the thyroid stimulating hormone receptor (TSHR) in humans. Our findings are further partially and indirectly supported by 3D docking results and literature information. The results based on approximately 500,000 interactions suggest that DRAMOTE has performed the best and that it can be used for developing robust virtual screening models. The datasets and implementation of all solutions are available as a MATLAB toolbox online at www.cbrc.kaust.edu.sa/dramote and can be found on Figshare.
CitationMining Chemical Activity Status from High-Throughput Screening Assays 2015, 10 (12):e0144426 PLOS ONE
PublisherPublic Library of Science (PLoS)
CollectionsArticles; Bioscience Program; Applied Mathematics and Computational Science Program; Physical Sciences and Engineering (PSE) Division; Computer Science Program; Chemical Science Program; KAUST Catalysis Center (KCC); Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
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