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Int. J. Mol. Sci. 2009, 10(7), 3106-3127; doi:10.3390/ijms10073106
Article

Additive SMILES-Based Carcinogenicity Models: Probabilistic Principles in the Search for Robust Predictions

1,2,* , 1,2
 and 2
Received: 14 May 2009; in revised form: 23 June 2009 / Accepted: 2 July 2009 / Published: 8 July 2009
(This article belongs to the Special Issue Recent Advances in QSAR/QSPR Theory)
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Abstract: Optimal descriptors calculated with the simplified molecular input line entry system (SMILES) have been utilized in modeling of carcinogenicity as continuous values (logTD50). These descriptors can be calculated using correlation weights of SMILES attributes calculated by the Monte Carlo method. A considerable subset of these attributes includes rare attributes. The use of these rare attributes can lead to overtraining. One can avoid the influence of the rare attributes if their correlation weights are fixed to zero. A function, limS, has been defined to identify rare attributes. The limS defines the minimum number of occurrences in the set of structures of the training (subtraining) set, to accept attributes as usable. If an attribute is present less than limS, it is considered “rare”, and thus not used. Two systems of building up models were examined: 1. classic training-test system; 2. balance of correlations for the subtraining and calibration sets (together, they are the original training set: the function of the calibration set is imitation of a preliminary test set). Three random splits into subtraining, calibration, and test sets were analysed. Comparison of abovementioned systems has shown that balance of correlations gives more robust prediction of the carcinogenicity for all three splits (split 1: rtest2=0.7514, stest=0.684; split 2: rtest2=0.7998, stest=0.600; split 3: rtest2=0.7192, stest=0.728).
Keywords: QSAR; SMILES; optimal descriptor; carcinogenicity; balance of correlations; applicability domain QSAR; SMILES; optimal descriptor; carcinogenicity; balance of correlations; applicability domain
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Toropov, A.A.; Toropova, A.P.; Benfenati, E. Additive SMILES-Based Carcinogenicity Models: Probabilistic Principles in the Search for Robust Predictions. Int. J. Mol. Sci. 2009, 10, 3106-3127.

AMA Style

Toropov AA, Toropova AP, Benfenati E. Additive SMILES-Based Carcinogenicity Models: Probabilistic Principles in the Search for Robust Predictions. International Journal of Molecular Sciences. 2009; 10(7):3106-3127.

Chicago/Turabian Style

Toropov, Andrey A.; Toropova, Alla P.; Benfenati, Emilio. 2009. "Additive SMILES-Based Carcinogenicity Models: Probabilistic Principles in the Search for Robust Predictions." Int. J. Mol. Sci. 10, no. 7: 3106-3127.


Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert