AIMC Topic: Ubiquitin

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NMR spectrum reconstruction as a pattern recognition problem.

Journal of magnetic resonance (San Diego, Calif. : 1997)
A new deep neural network based on the WaveNet architecture (WNN) is presented, which is designed to grasp specific patterns in the NMR spectra. When trained at a fixed non-uniform sampling (NUS) schedule, the WNN benefits from pattern recognition of...

Systematic prediction of degrons and E3 ubiquitin ligase binding via deep learning.

BMC biology
BACKGROUND: Degrons are short linear motifs, bound by E3 ubiquitin ligase to target protein substrates to be degraded by the ubiquitin-proteasome system. Mutations leading to deregulation of degron functionality disrupt control of protein abundance d...

Computed structures of core eukaryotic protein complexes.

Science (New York, N.Y.)
Protein-protein interactions play critical roles in biology, but the structures of many eukaryotic protein complexes are unknown, and there are likely many interactions not yet identified. We take advantage of advances in proteome-wide amino acid coe...

Time-resolved in vivo ubiquitinome profiling by DIA-MS reveals USP7 targets on a proteome-wide scale.

Nature communications
Mass spectrometry (MS)-based ubiquitinomics provides system-level understanding of ubiquitin signaling. Here we present a scalable workflow for deep and precise in vivo ubiquitinome profiling, coupling an improved sample preparation protocol with dat...

A Machine Learning Protocol for Predicting Protein Infrared Spectra.

Journal of the American Chemical Society
Infrared (IR) absorption provides important chemical fingerprints of biomolecules. Protein secondary structure determination from IR spectra is tedious since its theoretical interpretation requires repeated expensive quantum-mechanical calculations i...

Discovery of gene module acting on ubiquitin-mediated proteolysis pathway by co-expression network analysis for endometriosis.

Reproductive biomedicine online
RESEARCH QUESTION: Is abnormal gene module expression in the eutopic endometrium related to the occurrence of endometriosis?

Machine Learning Driven Analysis of Large Scale Simulations Reveals Conformational Characteristics of Ubiquitin Chains.

Journal of chemical theory and computation
Understanding the conformational characteristics of protein complexes in solution is crucial for a deeper insight in their biological function. Molecular dynamics simulations performed on high performance computing plants and with modern simulation t...

A novel method for the rapid detection of post-translationally modified visinin-like protein 1 in rat models of brain injury.

Brain injury
BACKGROUND: Although elevated serum levels of visinin-like protein 1 (VILIP-1), a neuron-specific calcium sensor protein, are associated with ischaemic stroke, only a single study has evaluated VILIP-1 as a biomarker of traumatic brain injury (TBI). ...

UbiSite: incorporating two-layered machine learning method with substrate motifs to predict ubiquitin-conjugation site on lysines.

BMC systems biology
BACKGROUND: The conjugation of ubiquitin to a substrate protein (protein ubiquitylation), which involves a sequential process--E1 activation, E2 conjugation and E3 ligation, is crucial to the regulation of protein function and activity in eukaryotes....