Probing the structures of amyloid-β (Aβ) peptides in the early steps of aggregation is extremely difficult experimentally and computationally. Yet, this knowledge is extremely important as small oligomers are the most toxic species. Experiments and s...
The non-coding RNA secondary structure largely determines its function. Hence, accuracy in structure acquisition is of great importance. Currently, this acquisition primarily relies on various computational methods. The prediction of the structures o...
IEEE/ACM transactions on computational biology and bioinformatics
Dec 8, 2022
Protein-DNA interactions play an important role in diverse biological processes. Accurately identifying protein-DNA binding residues is a critical but challenging task for protein function annotations and drug design. Although wet-lab experimental me...
The protein secondary structure (SS) prediction plays an important role in the characterization of general protein structure and function. In recent years, a new generation of algorithms for SS prediction based on embeddings from protein language mod...
Interdisciplinary sciences, computational life sciences
Nov 8, 2022
PURPOSE: The determination of which amino acid in a protein interacts with other proteins is important in understanding the functional mechanism of that protein. Although there are experimental methods to detect protein-protein interaction sites (PPI...
BACKGROUND: RNA Secondary Structure (RSS) has drawn growing concern, both for their pivotal roles in RNA tertiary structures prediction and critical effect in penetrating the mechanism of functional non-coding RNA. Computational techniques that can r...
BACKGROUND: RNA secondary structure is very important for deciphering cell's activity and disease occurrence. The first method which was used by the academics to predict this structure is biological experiment, But this method is too expensive, causi...
Proteins are constructed from amino acid sequences. Their structural classifications include primary, secondary, tertiary, and quaternary, with tertiary and quaternary structures influencing protein function. Because a protein's structure is inextric...
The binding and catalytic functions of proteins are generally mediated by a small number of functional residues held in place by the overall protein structure. Here, we describe deep learning approaches for scaffolding such functional sites without n...
The assignment of secondary structure elements in protein conformations is necessary to interpret a protein model that has been established by computational methods. The process essentially involves labeling the amino acid residues with H (Helix), E ...
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