AIMC Topic: Proteome

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Backyard Proteomics: A Case Study with the Black Widow Spider.

Journal of proteome research
Nearly all methods of mass-spectrometry-based proteomics rely on knowing the proteome of the species. In less studied organisms without annotated genomes, it can seem impossible to perform proteomic analysis. In this study, we sought to answer the qu...

Circulating Proteomic Panels for Noninvasive Diagnosis and Prognostication of Thromboangiitis Obliterans.

Journal of proteome research
Thromboangiitis obliterans (TAO) is often diagnosed late and characterized by high amputation rates. TAO-specific early diagnostic and disease-staging biomarkers are urgently needed. A staged mass spectrometry (MS)-based discovery-verification-valida...

TopCysteineDB: A Cysteinome-wide Database Integrating Structural and Chemoproteomics Data for Cysteine Ligandability Prediction.

Journal of molecular biology
Development of targeted covalent inhibitors and covalent ligand-first approaches have emerged as a powerful strategy in drug design, with cysteines being attractive targets due to their nucleophilicity and relative scarcity. While structural biology ...

Uncovering hepatic transcriptomic and circulating proteomic signatures in MASH: A meta-analysis and machine learning-based biomarker discovery.

Computers in biology and medicine
BACKGROUND: Metabolic-associated steatohepatitis (MASH), the progressive form of metabolic-associated steatotic liver disease (MASLD), poses significant risks for liver fibrosis and cardiovascular complications. Despite extensive research, reliable b...

[Serum proteomics and machine learning unveil new diagnostic biomarkers for tuberculosis in adolescents and young adults].

Sheng wu gong cheng xue bao = Chinese journal of biotechnology
Adolescents and young adults (AYAs) are one of the major populations susceptible to tuberculosis. However, little is known about the unique characteristics and diagnostic biomarkers of tuberculosis in this population. In this study, 81 AYAs were recr...

AtSubP-2.0: An integrated web server for the annotation of Arabidopsis proteome subcellular localization using deep learning.

The plant genome
The organization of subcellular components in a cell is critical for its function and studying cellular processes, protein-protein interactions, identifying potential drug targets, network analysis, and other systems biology mechanisms. Determining p...

UniProt: the Universal Protein Knowledgebase in 2025.

Nucleic acids research
The aim of the UniProt Knowledgebase (UniProtKB; https://www.uniprot.org/) is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this publication, we describe o...

OrgXenomics: an integrated proteomic knowledge base for patient-derived organoid and xenograft.

Nucleic acids research
Patient-derived models (PDMs, particularly organoids and xenografts) are irreplaceable tools for precision medicine, from target development to lead identification, then to preclinical evaluation, and finally to clinical decision-making. So far, PDM-...

Artificial intelligence and omics-based autoantibody profiling in dementia.

Frontiers in immunology
INTRODUCTION: Dementia is a neurodegenerative syndrome marked by the accumulation of disease-specific proteins and immune dysregulation, including autoimmune mechanisms involving autoantibodies. Current diagnostic methods are often invasive, time-con...

Sitetack: a deep learning model that improves PTM prediction by using known PTMs.

Bioinformatics (Oxford, England)
MOTIVATION: Post-translational modifications (PTMs) increase the diversity of the proteome and are vital to organismal life and therapeutic strategies. Deep learning has been used to predict PTM locations. Still, limitations in datasets and their ana...