Trypsin is one of the most important and widely used proteolytic enzymes in mass spectrometry (MS)-based proteomic research. It exclusively cleaves peptide bonds at the C-terminus of lysine and arginine. However, the cleavage is also affected by seve...
Mass spectrometry data sets from omics studies are an optimal information source for discriminating patients with disease and identifying biomarkers. Thousands of proteins or endogenous metabolites can be queried in each analysis, spanning several or...
In cross-linking mass spectrometry, the identification of cross-linked peptide pairs heavily relies on the ability of a database search engine to measure the similarities between experimental and theoretical MS/MS spectra. However, the lack of accura...
Identification of phosphorylation sites is an important step in the function study and drug design of proteins. In recent years, there have been increasing applications of the computational method in the identification of phosphorylation sites becaus...
A model that predicts levels of coronavirus (CoV) respiratory and fecal-oral transmission potentials based on the shell disorder has been built using neural network (artificial intelligence, AI) analysis of the percentage of disorder (PID) in the nuc...
As hormones in the endocrine system and neurotransmitters in the immune system, neuropeptides (NPs) provide many opportunities for the discovery of new drugs and targets for nervous system disorders. In spite of their importance in the hormonal regul...
There have been more than 2.2 million confirmed cases and over 120 000 deaths from the human coronavirus disease 2019 (COVID-19) pandemic, caused by the novel severe acute respiratory syndrome coronavirus (SARS-CoV-2), in the United States alone. How...
Deep learning (DL), a type of machine learning approach, is a powerful tool for analyzing large sets of data that are derived from biomedical sciences. However, it remains unknown whether DL is suitable for identifying contributing factors, such as b...
The large-scale identification of protein-protein interactions (PPIs) between humans and bacteria remains a crucial step in systematically understanding the underlying molecular mechanisms of bacterial infection. Computational prediction approaches a...
Despite the increasing use of high-throughput experiments in molecular biology, methods for evaluating and classifying the acquired results have not kept pace, requiring significant manual efforts to do so. Here, we present CiRCus, a framework to gen...