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Mapping conformational landscape in protein folding: Benchmarking dimensionality reduction and clustering techniques on the Trp-Cage mini-protein.
Biophys Chem
January 2025
Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, India. Electronic address:
Quantitative characterization of protein conformational landscapes is a computationally challenging task due to their high dimensionality and inherent complexity. In this study, we systematically benchmark several widely used dimensionality reduction and clustering methods to analyze the conformational states of the Trp-Cage mini-protein, a model system with well-documented folding dynamics. Dimensionality reduction techniques, including Principal Component Analysis (PCA), Time-lagged Independent Component Analysis (TICA), and Variational Autoencoders (VAE), were employed to project the high-dimensional free energy landscape onto 2D spaces for visualization.
View Article and Find Full Text PDFUltralow Coordination Copper Sites Compartmentalized within Ordered Pores for Highly Efficient Electrosynthesis of -Propanol from CO.
J Am Chem Soc
January 2025
Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China.
Coordinatively unsaturated copper (Cu) has been demonstrated to be effective for electrifying CO reduction into C products by adjusting the coupling of C-C intermediates. Nevertheless, the intuitive impacts of ultralow coordination Cu sites on C products are scarcely elucidated due to the lack of synthetic recipes for Cu with low coordination numbers and its vulnerability to aggregation under reductive potentials. Herein, computational predictions revealed that Cu sites with higher levels of coordinative unsaturation favored the adsorption of C and C intermediates.
View Article and Find Full Text PDFExploring the Pharmacogenomic Map of Croatia: PGx Clustering of 522-Patient Cohort Based on UMAP + HDBSCAN Algorithm.
Int J Mol Sci
January 2025
St. Catherine Specialty Hospital, 10000 Zagreb, Croatia.
Pharmacogenetics is a branch of genomic medicine aiming to personalize drug prescription guidelines based on individual genetic information. This concept might lead to a reduction in adverse drug reactions, which place a heavy burden on individual patients' health and the economy of the healthcare system. The aim of this study was to present insights gained from the pharmacogenetics-based clustering of over 500 patients from the Croatian population.
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