QSAR modeling is a method for predicting properties, e.g. the solubility or toxicity, of chemical compounds using statistical learning techniques. QSAR is in widespread use within the pharmaceutical industry to prioritize compounds for experimental testing or to alert for potential toxicity. However, predictions from a QSAR model are difficult to assess if their prediction intervals are unknown...

Measures of the irregularity of chemical graphs could be helpful for QSAR/QSPR studies and for the descriptive purposes of biological and chemical properties, such as melting and boiling points, toxicity and resistance. Here we consider the following four established irregularity measures: the irregularity index by Albertson, the total irregularity, the variance of vertex degrees and the Collat...

Shu Shen Liu, Hai Ling Liu, Yun Yu Shi, and Lian Sheng Wang 1 State Key Laboratory of Pollution Control and Resources Reuse, Department of Environmental Science & Engineering, Nanjing University, Nanjing 210093, P. R. China 2 Department of Applied Chemistry, Guilin Institute of Technology, Guilin 541004, P. R. China 3 Laboratory of Structural Biology, University of Science and Technology of Chi...

THE PHYSICAL AND chemical properties of a compound are a function of its molecular structure. Structure-property relationships are developed by finding one or more molecular descriptors that explain variations in the physical or chemical properties of a group of congeners/analogs. While some descriptors can be determined experimentally, deriving them from either the two-dimensional (2-D) or thr...

Previously reported rates of reaction between six mutant strains of the enzyme horseradish peroxidase (HRP) and a test substrate, 2-methoxyphenol, were found to correlate with characteristic binding distances computed using molecular simulation. The correlation (R(2) = 0.86) bears out a working hypothesis that, based on a quantitative structure-activity relationship (QSAR) we had previously dev...

Computer simulation and predictive models are widely used in engineering, much less considered in life sciences. We present an initiative aimed to establish a dialogue within the community of scientists, regulators, industry representatives, offering a platform which combines the predictive capability of computer models, with some explanation tools, which may be convincing and helpful for human...

Balaban index and Sum-Balaban index were used in various quantitative structureproperty relationship and quantitative structure activity relationship studies. In this paper, the unicyclic graphs with the second largest Balaban index and the second largest SumBalaban index among all unicyclic graphs on n vertices are characterized, respectively.

Computational chemistry and quantitative structureactivity relationships (QSAR) are foreseen to be extensively used in the implementation of the new REACH regulation for chemicals in Europe. However, for some compound groups the data are too few in number to permit both calibration and testing of a new model. Usage and previously developed or updated models are then viable alternatives. Perfluo...

The CDK framework provides a wide variety of cheminformatics functionality. Consequently a large variety of applications can be developed using this framework. One important application is the data mining of chemical information which requires a combination of cheminformatics and statistical tools. This article focusses on interfacing the CDK framework with the R [1] statistical environment for...