AIMC Topic: Proteome
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DeepBL: a deep learning-based approach for in silico discovery of beta-lactamases.
Briefings in bioinformatics
Jul 20, 2021
Beta-lactamases (BLs) are enzymes localized in the periplasmic space of bacterial pathogens, where they confer resistance to beta-lactam antibiotics. Experimental identification of BLs is costly yet crucial to understand beta-lactam resistance mechan...
Vaxign2: the second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning.
Nucleic acids research
Jul 2, 2021
Vaccination is one of the most significant inventions in medicine. Reverse vaccinology (RV) is a state-of-the-art technique to predict vaccine candidates from pathogen's genome(s). To promote vaccine development, we updated Vaxign2, the first web-bas...
Challenges of developing artificial intelligence-assisted tools for clinical medicine.
Journal of gastroenterology and hepatology
Feb 1, 2021
Machine learning, a subset of artificial intelligence (AI), is a set of computational tools that can be used to enhance provision of clinical care in all areas of medicine. Gastroenterology and hepatology utilize multiple sources of information, incl...
Can machine learning consistently improve the scoring power of classical scoring functions? Insights into the role of machine learning in scoring functions.
Briefings in bioinformatics
Jan 18, 2021
How to accurately estimate protein-ligand binding affinity remains a key challenge in computer-aided drug design (CADD). In many cases, it has been shown that the binding affinities predicted by classical scoring functions (SFs) cannot correlate well...
UniProt: the universal protein knowledgebase in 2021.
Nucleic acids research
Jan 8, 2021
The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this article, we describe significant updates that we have made over ...
Computational Phosphorylation Network Reconstruction: An Update on Methods and Resources.
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2021
Most proteins undergo some form of modification after translation, and phosphorylation is one of the most relevant and ubiquitous post-translational modifications. The succession of protein phosphorylation and dephosphorylation catalyzed by protein k...
Network Analysis of Integrin Adhesion Complexes.
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2021
Cell-surface adhesion receptors mediate interactions with the extracellular matrix (ECM) to control many fundamental aspects of cell behavior, including cell migration, survival, and proliferation. Integrin adhesion receptors recruit structural and s...
[Recent progress in capillary electrophoresis-based high-sensitivity proteomics].
Se pu = Chinese journal of chromatography
Oct 8, 2020
In recent years, proteomic techniques have undergone rapid progress in terms of sample pretreatment, separation, and mass spectrometry (MS) detection. The current MS-based proteomic techniques can be used to identify up to 10000 proteins both qualita...
Predicting bacterial virulence factors - evaluation of machine learning and negative data strategies.
Briefings in bioinformatics
Sep 25, 2020
Bacterial proteins dubbed virulence factors (VFs) are a highly diverse group of sequences, whose only obvious commonality is the very property of being, more or less directly, involved in virulence. It is therefore tempting to speculate whether their...
Machine learning predicts new anti-CRISPR proteins.
Nucleic acids research
May 21, 2020
The increasing use of CRISPR-Cas9 in medicine, agriculture, and synthetic biology has accelerated the drive to discover new CRISPR-Cas inhibitors as potential mechanisms of control for gene editing applications. Many anti-CRISPRs have been found that...
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