Chemical Graph Theory for Property Modeling in QSAR and QSPR—Charming QSAR & QSPR

Paulo C. S. Costa, Joel S. Evangelista, Igor Leal and Paulo C. M. L. Miranda
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Paulo C. S. Costa: Institute of Chemistry, University of Campinas—UNICAMP, Campinas, SP 13083-970, Brazil
Joel S. Evangelista: Institute of Chemistry, University of Campinas—UNICAMP, Campinas, SP 13083-970, Brazil
Igor Leal: Institute of Language Studies, University of Campinas—UNICAMP, Campinas, SP 13083-970, Brazil
Paulo C. M. L. Miranda: Institute of Chemistry, University of Campinas—UNICAMP, Campinas, SP 13083-970, Brazil

Mathematics, 2020, vol. 9, issue 1, 1-19

Abstract: Quantitative structure-activity relationship (QSAR) and Quantitative structure-property relationship (QSPR) are mathematical models for the prediction of the chemical, physical or biological properties of chemical compounds. Usually, they are based on structural (grounded on fragment contribution) or calculated (centered on QSAR three-dimensional (QSAR-3D) or chemical descriptors) parameters. Hereby, we describe a Graph Theory approach for generating and mining molecular fragments to be used in QSAR or QSPR modeling based exclusively on fragment contributions. Merging of Molecular Graph Theory, Simplified Molecular Input Line Entry Specification (SMILES) notation, and the connection table data allows a precise way to differentiate and count the molecular fragments. Machine learning strategies generated models with outstanding root mean square error (RMSE) and R 2 values. We also present the software Charming QSAR & QSPR , written in Python, for the property prediction of chemical compounds while using this approach.

Keywords: fragment based QSAR; fragment based QSPR; support vector machine; random forest; gradient boosting machine (search for similar items in EconPapers)
JEL-codes: C (search for similar items in EconPapers)
Date: 2020
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