A confidence predictor for logD using conformal regression and a support-vector machine

  • Lapins M
  • Arvidsson S
  • Lampa S
 et al. 
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Lipophilicity is a major determinant of ADMET properties and overall suitability of drug candidates. We have developed large-scale models to predict water–octanol distribution coefficient (logD) for chemical compounds, aiding drug discovery projects. Using ACD/logD data for 1.6 million compounds from the ChEMBL database, models are created and evaluated by a support-vector machine with a linear kernel using conformal prediction methodology, outputting prediction intervals at a specified confidence level. The resulting model shows a predictive ability of $$\hbox {Q}^{2}=0.973$$ Q 2 = 0.973 and with the best performing nonconformity measure having median prediction interval of $$\pm ~0.39$$ ± 0.39 log units at 80% confidence and $$\pm ~0.60$$ ± 0.60 log units at 90% confidence. The model is available as an online service via an OpenAPI interface, a web page with a molecular editor, and we also publish predictive values at 90% confidence level for 91 M PubChem structures in RDF format for download and as an URI resolver service.

Author-supplied keywords

  • Conformal prediction
  • LogD
  • Machine learning
  • QSAR
  • RDF
  • Support-vector machine

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