Methods in molecular biology (Clifton, N.J.)
Jan 1, 2022
The new flow of high-throughput RNA secondary structure data coming from different techniques allowed the further development of machine learning approaches. We developed CROSS and CROSSalive, two algorithms trained on experimental data able to predi...
The prediction of peptide secondary structures is fundamentally important to reveal the functional mechanisms of peptides with potential applications as therapeutic molecules. In this study, we propose a multi-view deep learning method named Peptide ...
Cryo-electron microscopy (cryo-EM) has become one of important experimental methods in structure determination. However, despite the rapid growth in the number of deposited cryo-EM maps motivated by advances in microscopy instruments and image proces...
Proceedings of the National Academy of Sciences of the United States of America
Jun 29, 2021
The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), invades a human cell via human angiotensin-converting enzyme 2 (hACE2) as the entry, causing the severe coronavirus disease (COVID-19). The interactions between hACE...
BACKGROUND: Interpretation of medical images for the diagnosis and treatment of complex diseases from high-dimensional and heterogeneous data remains a key challenge in transforming healthcare. In the last few years, both supervised and unsupervised ...
BACKGROUND: The prediction of a protein's secondary structure from its amino acid sequence is an essential step towards predicting its 3-D structure. The prediction performance improves by incorporating homologous multiple sequence alignment informat...
MOTIVATION: Predictions of protein backbone torsion angles (ϕ and ψ) and secondary structure from sequence are crucial subproblems in protein structure prediction. With the development of deep learning approaches, their accuracies have been significa...
MOTIVATION: Protein structures provide basic insight into how they can interact with other proteins, their functions and biological roles in an organism. Experimental methods (e.g. X-ray crystallography and nuclear magnetic resonance spectroscopy) fo...
MOTIVATION: RNA-protein interactions are key effectors of post-transcriptional regulation. Significant experimental and bioinformatics efforts have been expended on characterizing protein binding mechanisms on the molecular level, and on highlighting...
MOTIVATION: Protein structural annotations (PSAs) are essential abstractions to deal with the prediction of protein structures. Many increasingly sophisticated PSAs have been devised in the last few decades. However, the need for annotations that are...
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