Proteins are the key molecular machines that orchestrate all biological processes of the cell. Most proteins fold into three-dimensional shapes that are critical for their function. Studying the 3D shape of proteins can inform us of the mechanisms th...
Proceedings of the National Academy of Sciences of the United States of America
Jan 29, 2024
Amino acid mutations that lower a protein's thermodynamic stability are implicated in numerous diseases, and engineered proteins with enhanced stability can be important in research and medicine. Computational methods for predicting how mutations per...
Convolutional neural networks (CNNs) are currently among the most widely-used deep neural network (DNN) architectures available and achieve state-of-the-art performance for many problems. Originally applied to computer vision tasks, CNNs work well wi...
Over the last 15 years, structural biology has seen unprecedented development and improvement in two areas: electron cryo-microscopy (cryo-EM) and predictive modeling. Once relegated to low resolutions, single-particle cryo-EM is now capable of achie...
Journal of the American Society for Mass Spectrometry
Jan 23, 2024
Observed mass shifts associated with deuterium incorporation in hydrogen-deuterium exchange mass spectrometry (HDX-MS) frequently deviate from the initial signals due to back and forward exchange. In typical HDX-MS experiments, the impact of these di...
Small proteins (SPs) are a unique group of proteins that play crucial roles in many important biological processes. Exploring the biological function of SPs is necessary. In this study, the InterPro tool and the maximum correlation method were utiliz...
Journal of the American Chemical Society
Jan 19, 2024
The structurally sensitive amide II infrared (IR) bands of proteins provide valuable information about the hydrogen bonding of protein secondary structures, which is crucial for understanding protein dynamics and associated functions. However, deciph...
Journal of chemical theory and computation
Jan 12, 2024
Protein thermodynamics is intimately tied to biological function and can enable processes such as signal transduction, enzyme catalysis, and molecular recognition. The relative free energies of conformations that contribute to these functional equili...
Interdisciplinary sciences, computational life sciences
Jan 11, 2024
Long noncoding RNAs (lncRNAs) have significant regulatory roles in gene expression. Interactions with proteins are one of the ways lncRNAs play their roles. Since experiments to determine lncRNA-protein interactions (LPIs) are expensive and time-con...
Interdisciplinary sciences, computational life sciences
Jan 11, 2024
The protein S-nitrosylation (SNO) is a significant post-translational modification that affects the stability, activity, cellular localization, and function of proteins. Therefore, highly accurate prediction of SNO sites aids in grasping biological f...
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