A methodology for performing sequence-free comparison of functional sites in protein structures is introduced. The method is based on a new notion of similarity among superimposed groups of amino acid residues that evaluates both geometry and physico-chemical properties. The method is specifically designed to handle disconnected and sparsely distributed sets of residues. A genetic algorithm is employed to find the superimposition of protein segments that maximizes their similarity. The method was evaluated by performing an all-to-all comparison on two separate sets of ligand-binding sites, comprising 47 protein-FAD (Flavin-Adenine Dinucleotide) and 64 protein-NAD (Nicotinamide-Adenine Dinucleotide) complexes, and comparing the results with those of an existing sequence-based structural alignment tool (TM-Align). The quality of the two methodologies is judged by the methods' capacity to, among other, correctly predict the similarities in the protein-ligand contact patterns of each pair of binding sites. The results show that using a sequence-free method significantly improves over the sequence-based one, resulting in 23 significant binding-site homologies being detected by the new method but ignored by the sequence-based one.
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http://dx.doi.org/10.1016/j.compbiolchem.2015.12.004 | DOI Listing |
J Med Internet Res
January 2025
Learning and Capacity Development Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland.
Background: The COVID-19 pandemic demonstrated the global need for accessible content to rapidly train health care workers during health emergencies. The massive open access online course (MOOC) format is a broadly embraced strategy for widespread dissemination of trainings. Yet, barriers associated with technology access, language, and cultural context limit the use of MOOCs, particularly in lower-resource communities.
View Article and Find Full Text PDFJ Chem Inf Model
January 2025
School of Information and Artificial Intelligence, Anhui Provincial Engineering Research Center for Beidou Precision Agriculture Information, Key Laboratory of Agricultural Sensors for Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei, Anhui 230036, China.
Antimicrobial peptides (AMPs) are small peptides that play an important role in disease defense. As the problem of pathogen resistance caused by the misuse of antibiotics intensifies, the identification of AMPs as alternatives to antibiotics has become a hot topic. Accurately identifying AMPs using computational methods has been a key issue in the field of bioinformatics in recent years.
View Article and Find Full Text PDFNicotine Tob Res
January 2025
Department of Population Health Sciences, University of Leicester, Leicester, UK.
Introduction: Varenicline is an α4β2 nicotinic acetylcholine receptor partial agonist with the highest therapeutic efficacy of any pharmacological smoking cessation aid and a 12-month cessation rate of 26%. Genetic variation may be associated with varenicline response, but to date no genome-wide association studies of varenicline response have been published.
Methods: In this study, we investigated the genetic contribution to varenicline effectiveness using two electronic health record-derived phenotypes.
Microb Genom
January 2025
Center for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands.
Genes encoding OXA-48-like carbapenem-hydrolyzing enzymes are often located on plasmids and are abundant among carbapenemase-producing (CPE) worldwide. After a large plasmid-mediated outbreak in 2011, routine screening of patients at risk of CPE carriage on admission and every 7 days during hospitalization was implemented in a large hospital in the Netherlands. The objective of this study was to investigate the dynamics of the hospitals' 2011 outbreak-associated plasmid among CPE collected from 2011 to 2021.
View Article and Find Full Text PDFLangmuir
January 2025
School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China.
The lateral flow assay is a strip-based analytical method for the portable and convenient detection of analytes of interest. It has the advantages of visual observation, autonomous sample flow, fast coloration time, minimal tedious operation procedures, and reliance on specialized instruments. However, the rough surface of the nitrocellulose membrane renders it difficult for the immobilized nucleic acids to remain in an ordered arrangement, and the immobilized nucleic acids are also liable to be digested in a complex matrix, inducing limited sensitivity and anti-interference.
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