Cross-validation pitfalls when selecting and assessing regression and classification models.

Background: We address the problem of selecting and assessing classification and regression models using cross-validation. Current state-of-the-art methods can yield models with high variance, rendering them unsuitable for a number of practical applications including QSAR. In this paper we describe and evaluate best practices which improve reliability and increase confidence in selected models.

Chemical Descriptors Library (CDL): a generic, open source software library for chemical informatics.

In this article the Chemical Descriptors Library (CDL), a generic, open source software library for chemical informatics is introduced. The library is written using standard-compliant C++ programming language. The CDL provides a generic interface for traversing the structure of a molecular graph and accessing its properties.

Competitive Workflow: novel software architecture for automating drug design.

As industrialization of laboratory processes for drug discovery continues to gather momentum, the bottleneck has moved toward exploitation of this tide of information to enable better quality decisions. The development of information-management systems to automate data and materials management can have a positive impact on productivity, as can increasingly sophisticated computer-aided molecular design approaches. However, as long as key decisions can only be taken by a small number of expert individuals working in a complex social environment, the impact of such innovations will be limited.

Integrating in vitro ADMET data through generic physiologically based pharmacokinetic models.

Early estimation of kinetics in man currently relies on extrapolation from experimental data generated in animals. Recent results from the application of a generic physiologically based model, Cloe PK) (Cyprotex), which is parameterised for human and rat physiology, to the estimation of plasma pharmacokinetics, are summarised in this paper. A comparison with predictive methods that involve scaling from in vivo animal data can also be made from recently published data.

Prediction of in vivo tissue distribution from in vitro data. 3. Correlation between in vitro and in vivo tissue distribution of a homologous series of nine 5-n-alkyl-5-ethyl barbituric acids.

Purpose: To evaluate the ability to determine accurate in vivo tissue-to-unbound plasma distribution coefficients (Kpue) from in vitro data.

Methods: Fresh pieces of fifteen rat tissues/organs were incubated at 37 degrees C with a homologous series of nine barbiturates covering a wide range of lipophilicity (Log P 0.02 to 4.

Prediction of in vivo tissue distribution from in vitro data. 2. Influence of albumin diffusion from tissue pieces during an in vitro incubation on estimated tissue-to-unbound plasma partition coefficients (Kpu).

Purpose: To determine the extent of albumin diffusion from tissue pieces into medium during in vitro incubations, to develop and assess the utility of mathematical models describing this effect on the estimation of tissue-to-unbound plasma partition coefficients (Kpu) of drug substances and to derive factors to correct for associated errors.

Methods: Twelve separate tissues were obtained from rats sacrificed by cervical dislocation, 48 h after an intravenous dose of 125I-human albumin, and tissue pieces incubated to determine the efflux of albumin into media over 2 to 4 h. A mathematical model was developed to predict and correct for the effect of albumin diffusion on the measured Kpu values of drugs.

Progress in simulation modelling for pharmacokinetics.

Simulation models for the prediction of pharmacokinetics in humans and other mammalian species, which are based on the physiology and mechanistic models of absorption, distribution, metabolism and elimination are reviewed. The structure of such models is explained with reference to papers describing the mathematical details and alternative representations of organ flow and distribution. Approaches to the modelling of more complex tissues such as tumours and the liver are also reviewed as well as some specific transport processes such as biliary secretion and methods of ADME property estimation by experimental and in silico models.