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BaNDyT: Bayesian Network Modeling of Molecular Dynamics Trajectories.
J Chem Inf Model
January 2025
Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, California 91016, United States.
Bayesian network modeling (BN modeling, or BNM) is an interpretable machine learning method for constructing probabilistic graphical models from the data. In recent years, it has been extensively applied to diverse types of biomedical data sets. Concurrently, our ability to perform long-time scale molecular dynamics (MD) simulations on proteins and other materials has increased exponentially.
View Article and Find Full Text PDFHighly Selective α-Addition and β-Conjugate Addition Products from Peptides Composed of α,β-Unsaturated γ-Amino Acids.
J Org Chem
January 2025
Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India.
β-Addition products are common in conjugate addition reactions consisting of α,β-unsaturated carbonyl compounds. Here, we are reporting an uncommon α-addition product as a major product in the thioacetic acid conjugate addition reaction on a peptide consisting of ()-α,β-unsaturated γ-amino acids. In addition, we observed highly diastereoselective β-addition products from the thiophenol and thioethanol conjugate addition reaction on peptides.
View Article and Find Full Text PDF[Nephrology : what's new in 2024 (II)].
Rev Med Suisse
January 2025
Service de néphrologie, Département de médecine, Hôpitaux universitaires de Genève, Genève 14.
Certain molecules, such as GLP-1 agonists and endothelin antagonists, possess nephroprotective properties. When treating IgA nephropathy, endothelin antagonists and sibeprenlimab have shown effectiveness in slowing the progression of chronic kidney isease. Additionally, the infusion of amino acids can reduce the incidence of mild acute kidney injury following cardiac surgery.
View Article and Find Full Text PDFDissecting AlphaFold2's capabilities with limited sequence information.
Bioinform Adv
November 2024
Institute of Biochemistry and Molecular Medicine, University of Bern, Bern 3012, Switzerland.
Summary: Protein structure prediction aims to infer a protein's three-dimensional (3D) structure from its amino acid sequence. Protein structure is pivotal for elucidating protein functions, interactions, and driving biotechnological innovation. The deep learning model AlphaFold2, has revolutionized this field by leveraging phylogenetic information from multiple sequence alignments (MSAs) to achieve remarkable accuracy in protein structure prediction.
View Article and Find Full Text PDFThe effect of acute branched-chain amino acids ingestion on rate of force development in different time intervals: a controlled crossover study.
Front Nutr
January 2025
School of Sports Training, Chengdu Sport University, Chengdu, China.
Background: Branched-chain amino acids (BCAAs) are widely used as sports nutrition supplements. However, their impact on the rate of force development (RFD), an indicator of explosive muscle strength, has not yet been validated. This study aimed to assess the impact of BCAA supplementation on the RFD in college basketball players during simulated games.
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