Binding proteins play a crucial role in biological systems by selectively interacting with specific molecules, such as DNA, RNA, or peptides, to regulate various cellular processes. Their ability to recognize and bind target molecules with high speci...
IEEE journal of biomedical and health informatics
Mar 6, 2025
T cell receptors (TCRs) play a crucial role in numerous immunotherapies targeting tumor cells. However, their acquisition and optimization present significant challenges, involving laborious and time-consuming wet lab experimental resource. Deep gene...
The decomposition of a biomolecular complex into domains is an important step to investigate biological functions and ease structure determination. A successful approach to do so is the SPECTRUS algorithm, which provides a segmentation based on spect...
Knowing which residues of a protein are important for its function is of paramount importance for understanding the molecular basis of this function and devising ways of modifying it for medical or biotechnological applications. Due to the difficulty...
Peptide sequencing via tandem mass spectrometry (MS/MS) is essential in proteomics. Unlike traditional database searches, deep learning excels at de novo peptide sequencing, even for peptides missing from existing databases. Current deep learning mod...
peptide sequencing is a valuable technique in mass-spectrometry-based proteomics, as it deduces peptide sequences directly from tandem mass spectra without relying on sequence databases. This database-independent method, however, relies solely on im...
IEEE/ACM transactions on computational biology and bioinformatics
Dec 10, 2024
Accurate identification of antifreeze proteins (AFPs) is crucial in developing biomimetic synthetic anti-icing materials and low-temperature organ preservation materials. Although numerous machine learning-based methods have been proposed for AFPs pr...
IEEE/ACM transactions on computational biology and bioinformatics
Dec 10, 2024
Deep learning approaches, such as convolution neural networks (CNNs) and deep recurrent neural networks (RNNs), have been the backbone for predicting protein function, with promising state-of-the-art (SOTA) results. RNNs with an in-built ability (i) ...
Journal of computational biology : a journal of computational molecular cell biology
Oct 23, 2024
De novo protein sequencing is an important problem in proteomics, playing a crucial role in understanding protein functions, drug discovery, design and evolutionary studies, etc. Top-down and bottom-up tandem mass spectrometry are popular approaches ...
Interactions of biological molecules in organisms are considered to be primary factors for the lifecycle of that organism. Various important biological functions are dependent on such interactions and among different kinds of interactions, the protei...
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