title: In silico prediction of chemical Ames mutagenicity.
abstract: Mutagenicity is one of the most important end points of toxicity. Due to high cost and laboriousness in experimental tests, it is necessary to develop robust in silico methods to predict chemical mutagenicity. In this paper, a comprehensive database containing 7617 diverse compounds, including 4252 mutagens and 3365 nonmutagens, was constructed. On the basis of this data set, high predictive models were then built using five machine learning methods, namely support vector machine (SVM), C4.5 decision tree (C4.5 DT), artificial neural network (ANN), k-nearest neighbors (kNN), and naïve Bayes (NB), along with five fingerprints, namely CDK fingerprint (FP), Estate fingerprint (Estate), MACCS keys (MACCS), PubChem fingerprint (PubChem), and Substructure fingerprint (SubFP). Performances were measured by cross validation and an external test set containing 831 diverse chemicals. Information gain and substructure analysis were used to interpret the models. The accuracies of fivefold cross validation were from 0.808 to 0.841 for top five models. The range of accuracy for the external validation set was from 0.904 to 0.980, which outperformed that of Toxtree. Three models (PubChem-kNN, MACCS-kNN, and PubChem-SVM) showed high and reliable predictive accuracy for the mutagens and nonmutagens and, hence, could be used in prediction of chemical Ames mutagenicity.
authors.affiliation: Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.
authors.forename: Congying
authors.initials: C
authors.lastname: Xu
authors.forename: Feixiong
authors.initials: F
authors.lastname: Cheng
authors.forename: Lei
authors.initials: L
authors.lastname: Chen
authors.forename: Zheng
authors.initials: Z
authors.lastname: Du
authors.forename: Weihua
authors.initials: W
authors.lastname: Li
authors.forename: Guixia
authors.initials: G
authors.lastname: Liu
authors.forename: Philip W
authors.initials: PW
authors.lastname: Lee
authors.forename: Yun
authors.initials: Y
authors.lastname: Tang
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D003198:Computer Simulation; D062126:Databases, Chemical; D003663:Decision Trees; D006801:Humans; D009152:Mutagenicity Tests / Q000379:methods* / Q000706:statistics & numerical data; D009153:Mutagens / Q000737:chemistry* / Q000633:toxicity*; D016571:Neural Networks, Computer; D011237:Predictive Value of Tests; D021281:Quantitative Structure-Activity Relationship; D015203:Reproducibility of Results; D060388:Support Vector Machine
chemical_list: D009153:Mutagens