Carcinogenic activity has been investigated using the Radial-Distribution-Function (RDF) approach. A discriminant model was developed to predict the carcinogenic and non-carcinogenic activity on a data set of 188 compounds. The percentage of overall classification was 76.4% for the carcinogenic chemicals and 72.5% for the non-carcinogenic chemicals. The predictive power of the model was validated by two tests: a cross-validation by the resubstitution technique and a test set (compounds not used in the development of the model) with 79.3 and 72.5% good classification, respectively. The RDF descriptors were compared with eight other methodologies; Constitutional, Molecular walks counts, Galvez topological charge indices, 2D autocorrelations, Randić molecular profiles, Geometrical, 3D-MORSE, and WHIM, demonstrating that the RDF descriptors are better to the rest of the approaches used.

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00894-005-0088-5DOI Listing

Publication Analysis

Top Keywords

rdf descriptors
8
radial-distribution-function approach
4
approach predicting
4
predicting rodent
4
rodent carcinogenicity
4
carcinogenicity carcinogenic
4
carcinogenic activity
4
activity investigated
4
investigated radial-distribution-function
4
radial-distribution-function rdf
4

Similar Publications

The toxicity of chemical mixtures may be misestimated, as the assessment of individual chemicals may not adequately reflect their combined toxic effects. However, numerous combinations of chemicals and various interactions make it impossible to measure all possible mixtures. Computational toxicology can help to mitigate this issue, particularly with new methodologies that rely upon alternatives to animal testing.

View Article and Find Full Text PDF

OrthoDB and BUSCO update: annotation of orthologs with wider sampling of genomes.

Nucleic Acids Res

January 2025

Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland, and Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland.

OrthoDB (https://www.orthodb.org) offers evolutionary and functional annotations of orthologous genes in the widest sampling of eukaryotes, prokaryotes, and viruses, extending experimental gene function knowledge to newly sequenced genomes.

View Article and Find Full Text PDF
Article Synopsis
  • Machine learning techniques, specifically principal component analysis (PCA) and diffusion maps (DM), are used to analyze complex datasets from molecular dynamics simulations of polylactide (PLA) and poly(3-hydroxybutyrate) (PHB) to evaluate glass transition temperature (Tg).
  • Four molecular descriptors—radial distribution functions (RDFs), mean square displacements (MSDs), relative square displacements (RSDs), and dihedral angles (DAs)—are employed to facilitate this evaluation.
  • The use of Gaussian Mixture Models (GMMs) to analyze the data reveals a clear distinction between melt and glass states and shows that Tg values derived from DM and certain descriptors align well with
View Article and Find Full Text PDF

This study presents a comprehensive framework to enhance Wikidata as an open and collaborative knowledge graph by integrating Open Biological and Biomedical Ontologies (OBO) and Medical Subject Headings (MeSH) keywords from PubMed publications. The primary data sources include OBO ontologies and MeSH keywords, which were collected and classified using SPARQL queries for RDF knowledge graphs. The semantic alignment between OBO ontologies and Wikidata was evaluated, revealing significant gaps and distorted representations that necessitate both automated and manual interventions for improvement.

View Article and Find Full Text PDF

The exclusion mechanism of food contaminants such as bisphenol A (BPA), Flavonoids (FLA), and Goitrin (GOI) onto the novel gallium-metal organic framework (MOF) and functionalized MOF with oxalamide group (MOF-OX) is evaluated by utilizing molecular dynamics (MD) and Metadynamics simulations. The atoms in molecules (AIM) analysis detected different types of atomic interactions between contaminant molecules and substrates. To assess this procedure, a range of descriptors including interaction energies, root mean square displacement, radial distribution function (RDF), density, hydrogen bond count (HB), and contact numbers are examined across the simulation trajectories.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!