Chemoinformatics in drug Discovery
The models were built using the Leadscope Predictive Data Miner software and the training data sets were compiled at the US Food and Drug Administration (FDA) by the Division of Drugs Safety Research (DDSR). The QSAR models are implemented with molecular descriptors that include structural features and 7 calculated properties. The structural features include a set selected from Leadscope's 27, 000 pre-defined structural features, predictive scaffolds (larger structural features that show association to the toxicity endpoint) and structural alerts identified from the literature. The seven calculated properties used are: parent molecular weight, aLogP, polar surface area, hydrogen bond acceptors, hydrogen bond donors, number of rotational bonds and Lipinski score (rule violation). The QSAR models are built using the structural feature and properties as descriptors also described as x- or independent variables. The models encode the relationship between these descriptors and the toxicity endpoint, such as the results of the bacterial mutagenesis assay (i.e, y- variable or response variable). The modeling technique used to generate these models is referred to as partial logistic regression.
When a prediction is made on a new chemical, the same structural features and properties in the model are calculated for the test compounds. These descriptors are then used with the models to calculate a probability of a positive result. See appendix A for more details.Does the Leadscope Model Applier methodology follow the validation principles set forth by the Organisation for Economic Co-operation and Development (OECD)?
I understand the statistical-based QSAR models are derived from a training set of historical results. How many chemicals does it include, where do they come from, and what sort of chemistries do they cover?
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An anecdotal responseby invivoVibrio
I have worked in several labs that have produced, either directly or through a spin-off company, real products that are medically useful. Scientists are the ones who create vaccines, design diagnostic devices and tests, and discover useful drugs.
There's a whole spectrum that falls under the title "science," which ranges from the purely discovery-oriented, focusing on just learning more about a topic for learning's sake; to the purely practical, such as so-called translational research, where scientists iron out the details of a practically useful discovery and optimize it for practical applications, "translating" the basic science into something that can be produced and sold by industry
Chemoinformatics in Drug Discovery
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