Citation: Stefaniak F (2015) Prediction of Compounds Activity in Nuclear Receptor Signaling and Stress Pathway Assays Using Machine Learning Algorithms and Low-Dimensional Molecular Descriptors. Front. Environ. Sci. 3:77. doi: 10.3389/fenvs.2015.00077 Prediction of Compounds Activity in Nuclear Receptor Signaling and Stress Pathway Assays Using Machine Learning Algorithms and Low-Dimensional Mo...

A novel set of molecular descriptors suitable for use in quantitative structure-activity relationships and related methods is described. These descriptors are a smooth and interpretable representation of atomic physicochemical property values and intramolecular atom pair distances. Distance atomic physicochemical parameter energy relationships (DAPPER), a novel structure-activity relationship (...

The logarithmic n-octanol/water partition coefficient (logK(ow)) is a very important property which concerns water-solubility, bioconcentration factor, toxicity and soil absorption coefficient of organic compounds. Quantitative structure-property relationship (QSPR) model for logK(ow) of 133 polychlorinated biphenyls (PCBs) is analyzed using heuristic method (HM) implemented in CODESSA. In orde...

New molecular descriptors based on statistical descriptions of the local ionization potential, local electron affinity and the local polarizability at the surface of the molecule are proposed. The significance of these descriptors has been tested by calculating them for the Maybridge database in addition to our set of 26 descriptors described previously. The new descriptors show little correlat...

The imprinting factors of the β-lactam antibiotics penicillin V, methicillin, nafcillin, oxacillin, cloxacillin, dicloxacillin, and piperacillin on a poly(methacrylic acid-co-trimethylolpropane trimethacrylate) molecularly imprinted stationary phase targeted for penicillin G were correlated with molecular descriptors obtained by molecular computation. One-parameter linear regression and multiva...

Descriptor properties are often neglected when building 3D-QSAR models. The relevance of correlation and distribution profiles is tested in terms of the models' prediction power. A different approach to filter descriptors prior to variable selection is proposed. Additionally, a protocol for molecular interaction field descriptors selection and model validation is presented. The algorithms and p...

A semiempirical molecular-orbital method (CAChe 4.9, PM5) was applied to delineate the relationship between the cytotoxicity (evaluated by 50% cytotoxic concentration, CC(50)) of nineteen 1,2,3,4-tetrahydroisoquinoline derivatives, their molecular weight and the sixteen chemical parameters (descriptors) determined by CONFLEX/PM5 method. There was little or no correlation between the CC(50) in H...

Novel atom-based molecular descriptors based on a bilinear map similar to use defined in linear algebra are presented. These molecular descriptors, called “local (atom, group and atom-type) and total (global) bilinear indices”, are proposed here as a new molecular parametrization easily calculated from the 2D molecular information. The proposed non-stochastic and stochastic molecular fingerprin...

Similarity search over chemical compound databases is a fundamental task in the discovery and design of novel drug-like molecules. Such databases often encode molecules as non-negative integer vectors, called molecular descriptors, which represent rich information on various molecular properties. While there exist efficient indexing structures for searching databases of binary vectors, solution...

The aim of the present paper is to present the methodology of the molecular descriptors family (MDF) as an integrative tool in molecular modeling and its abilities as a multivariate QSAR/QSPR modeling tool. An algorithm for extracting useful information from the topological and geometrical representation of chemical compounds was developed and integrated to calculate MDF members. The MDF method...