Confidence bands and hypothesis tests for hit enrichment curves.

In virtual screening for drug discovery, hit enrichment curves are widely used to assess the performance of ranking algorithms with regard to their ability to identify early enrichment. Unfortunately, researchers almost never consider the uncertainty associated with estimating such curves before declaring differences between performance of competing algorithms. Uncertainty is often large because the testing fractions of interest to researchers are small.

chemmodlab: a cheminformatics modeling laboratory R package for fitting and assessing machine learning models.

The goal of chemmodlab is to streamline the fitting and assessment pipeline for many machine learning models in R, making it easy for researchers to compare the utility of these models. While focused on implementing methods for model fitting and assessment that have been accepted by experts in the cheminformatics field, all of the methods in chemmodlab have broad utility for the machine learning community. chemmodlab contains several assessment utilities, including a plotting function that constructs accumulation curves and a function that computes many performance measures.

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Permeation of chemical solutes through skin can create major health issues. Using the membrane-coated fiber (MCF) as a solid phase membrane extraction (SPME) approach to simulate skin permeation, we obtained partition coefficients for 37 solutes under 90 treatment combinations that could broadly represent formulations that could be associated with occupational skin exposure. These formulations were designed to mimic fluids in the metalworking process, and they are defined in this manuscript using: one of mineral oil, polyethylene glycol-200, soluble oil, synthetic oil, or semi-synthetic oil; at a concentration of 0.

Analysis of High-Dimensional Structure-Activity Screening Datasets Using the Optimal Bit String Tree.

A new classification method called the Optimal Bit String Tree is proposed to identify quantitative structure-activity relationships (QSARs). The method introduces the concept of a to describe the presence/absence context of a combination of descriptors. A descriptor set and its optimal chromosome form the splitting variable.

Predicting skin permeability from complex chemical mixtures: incorporation of an expanded QSAR model.

Quantitative structure-activity relationship (QSAR) models have been widely used to study the permeability of chemicals or solutes through skin. Among the various QSAR models, Abraham's linear free-energy relationship (LFER) model is often employed. However, when the experimental conditions are complex, it is not always appropriate to use Abraham's LFER model with a single set of regression coefficients.