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.
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http://dx.doi.org/10.1007/s00894-005-0088-5 | DOI Listing |
Environ Res
December 2024
School of Urban Planning and Design, Peking University Shenzhen Graduate School, Shenzhen, 518055, China. Electronic address:
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 PDFNucleic 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 PDFJ Chem Phys
November 2024
Department of Physics and Astronomy, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7, Canada.
Heliyon
October 2024
Data Engineering and Semantics Research Unit, Faculty of Sciences of Sfax, University of Sfax, Sfax, Tunisia.
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 PDFSci Rep
August 2024
Department of Chemistry, University of Birjand, Birjand, Iran.
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.
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