Journal
MOLECULAR INFORMATICS
Volume 30, Issue 9, Pages 765-777Publisher
WILEY-V C H VERLAG GMBH
DOI: 10.1002/minf.201100092
Keywords
Drug design; Computational chemistry; Screening hit identification; High-throughput screening; Support vector machines; Balanced classification; Kernel functions; Molecular descriptors; Fast algorithms
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Funding
- Quebec Nature and Technology Research Fund
- United States National Institutes of Health [1P20HG003899-03]
- Rensselaer Center for Biotechnology and Interdisciplinary Studies (CBIS)
- Department of Mathematical Sciences at Rensselaer Polytechnic Institute
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Making suitable modeling choices is crucial for successful in silico drug design, and one of the most important of these is the proper extraction and curation of data from qHTS screens, and the use of optimized statistical learning methods to obtain valid models. More specifically, we aim to learn the top-1% most potent compounds against a variety of targets in a procedure we call virtual screening hit identification (VISHID). To do so, we exploit quantitative high-throughput screens (qHTS) obtained from PubChem, descriptors derived from molecular structures, and support vector machines (SVM) for model generation. Our results illustrate how an appreciation of subtle issues underlying qHTS data extraction and the resulting SVM models created using these data can enhance the effectiveness of solutions and, in doing so, accelerate drug discovery.
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