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Profile search methods based on protein domain alignments have proven to be useful tools in comparative sequence analysis. Domain alignments used by currently available search methods have been computed by sequence comparison. With the growth of the protein structure database, however, alignments of many domain pairs have also been computed by structure comparison. Here, we examine the extent to which information from these two sources agrees. We measure agreement with respect to identification of homologous regions in each protein, that is, with respect to the location of domain boundaries. We also measure agreement with respect to identification of homologous residue sites by comparing alignments and assessing the accuracy of the molecular models they predict. We find that domain alignments in publicly available collections based on sequence and structure comparison are largely consistent. However, the homologous regions identified by sequence comparison are often shorter than those identified by 3D structure comparison. In addition, when overall sequence similarity is low alignments from sequence comparison produce less accurate molecular models, suggesting that they less accurately identify homologous sites. These observations suggest that structure comparison results might be used to improve the overall accuracy of domain alignment collections and the performance of profile search methods based on them.
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http://dx.doi.org/10.1002/prot.10163 | DOI Listing |
Infect Drug Resist
December 2024
Department of Epidemiology and Health Statistics, School of Public Health, Xinxiang Medical University, Xinxiang, Henan Province, 453003, People's Republic of China.
Purpose: This study sets out to explore the forecasting value in syphilis incidence of the Bayesian structural time series (BSTS) model in Jiangsu Province.
Methods: The seasonal autoregressive integrated moving average (ARIMA) and BSTS models were constructed using the series from January 2017 to December 2021, and the prediction accuracy of both models was tested using the series from January 2022 to November 2022.
Results: From January 2017 to November 2022, the total number of syphilis cases in Jiangsu Province was 170629, with an average monthly notification cases of 2403.
ACS Earth Space Chem
December 2024
Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States.
As wildfire events become more frequent, there is a need to better understand the impact of smoke on the environment and human health. Smoke, or biomass burning aerosol (BBA), can undergo atmospheric processing changing its chemical and optical properties. We examined the interactions between four lignin pyrolysis products (catechol, syringol, syringic acid, and vanillic acid) and three BBA-relevant iron oxide mineral phases (hematite, maghemite, and magnetite) using attenuated total reflectance-Fourier transform infrared spectroscopy and dissolved iron measurements to better understand how atmospheric processing changes concentrations of soluble iron, iron oxidation state, and brown carbon abundance.
View Article and Find Full Text PDFACS Earth Space Chem
December 2024
School of Chemistry, The University of Edinburgh, Joseph Black Building, David Brewster Road, King's Buildings, Edinburgh EH9 3FJ, Scotland, U.K.
Identification of the molecular carriers of diffuse interstellar bands (DIBs) requires gas phase electronic spectra of suitable candidate structures. Recording the spectra of these in the laboratory is challenging because they include large, carbon-rich molecules, many of which are likely to be ionic. The electronic spectra of ions are often obtained using action spectroscopy methods, which can induce small perturbations to the absorption characteristics and hinder comparison with astronomical observations.
View Article and Find Full Text PDFHeliyon
December 2024
Evolved.Bio, 280 Joseph Street, Kitchener, Ontario, Canada.
Omics techniques, such as proteomics, contain crucial data for understanding biological processes, but they remain underutilized due to their high dimensionality. Typically, proteomics research focuses narrowly on using a limited number of datasets, hindering cross-study comparisons, a problem that can potentially be addressed by machine learning. Despite this potential, machine learning has seen limited adoption in the field of proteomics.
View Article and Find Full Text PDFBiochem Biophys Res Commun
December 2024
Department of Dairy, Fat and Cosmetics, University of Chemistry and Technology in Prague, Technická 5, 166 28, Prague, Czech Republic.
Galactooligosaccharides (GOS) are lactose-derived functional ingredients applied in food products and have great potential in health protection. The conversion of lactose to GOS commonly occurs using β-galactosidases of mould, yeast and bacterial origin. The yield and structure of the resulting GOS depend on the enzyme used and the reaction conditions.
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