Computational target identification plays a pivotal role in the drug development process. With the significant advancements of deep learning methods for protein structure prediction, the structural coverage of human proteome has increased substantial...
The first step in bottom-up proteomics is the assignment of measured fragmentation mass spectra to peptide sequences, also known as peptide spectrum matches. In recent years novel algorithms have pushed the assignment to new heights; unfortunately, d...
Current opinion in structural biology
Jan 22, 2025
Proteome-scale interaction prediction is essential for understanding protein functions and disease mechanisms. Traditional experimental methods are often limited by scale and complexity, driving the need for computational approaches. Deep learning ha...
Frontiers in cellular and infection microbiology
Jan 13, 2025
INTRODUCTION: This study aims to utilize proteomics, bioinformatics, and machine learning algorithms to identify diagnostic biomarkers in the serum of patients with acute and chronic brucellosis.
Proteome changes associated with APOE4 variant carriage that are independent of Alzheimer's disease (AD) pathology and diagnosis are unknown. This study investigated APOE4 proteome changes in people with AD, mild cognitive impairment, and no impairme...
Recent years have witnessed the remarkable progress of deep learning within the realm of scientific disciplines, yielding a wealth of promising outcomes. A prominent challenge within this domain has been the task of predicting enzyme function, a comp...
The gut microbiota is a crucial link between diet and cardiovascular disease (CVD). Using fecal metaproteomics, a method that concurrently captures human gut and microbiome proteins, we determined the crosstalk between gut microbiome, diet, gut healt...
International journal of molecular sciences
Dec 21, 2024
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a member of the large coronavirus family with high infectivity and pathogenicity and is the primary pathogen causing the global pandemic of coronavirus disease 2019 (COVID-19). Phosphory...
Biomolecular condensates are membraneless organelles that can concentrate hundreds of different proteins in cells to operate essential biological functions. However, accurate identification of their components remains challenging and biased towards p...
Journal of agricultural and food chemistry
Nov 13, 2024
Proteomics can be used to assess individual protein abundances, which could reflect genotypic and environmental effects and potentially predict grain/malt quality. In this study, 79 barley grain samples (genotype-location-year combinations) from Cali...
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