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FID-Net: A versatile deep neural network architecture for NMR spectral reconstruction and virtual decoupling
Apr 19, 2021 - 10:30 AM - by nmrlearner
nmrlearner's Avatar FID-Net: A versatile deep neural network architecture for NMR spectral reconstruction and virtual decoupling

Abstract

In recent years, the transformative potential of deep neural networks (DNNs) for analysing and interpreting NMR data has clearly been recognised. However, most applications of DNNs in NMR to date either struggle to outperform existing methodologies or are limited in scope to a narrow range of data that closely resemble the data that the network was trained on. These limitations have prevented a widescale uptake of DNNs in NMR. Addressing this, we introduce FID-Net, a deep neural network architecture inspired by WaveNet, for performing analyses on time domain NMR data. We first demonstrate the effectiveness of this architecture in reconstructing non-uniformly sampled (NUS) biomolecular NMR spectra. It is shown that a single network is able to reconstruct a diverse range of 2D NUS spectra that have been obtained with arbitrary sampling schedules, with a range of sweep widths, and a variety of other acquisition parameters. The performance of the trained FID-Net in this case exceeds or matches existing methods currently used for the reconstruction of NUS NMR spectra. Secondly, we present a network based on the FID-Net architecture that can efficiently virtually decouple 13Cα-13Cβ couplings in HNCA protein NMR spectra in a single shot analysis, while at the same time leaving glycine residues unmodulated. The ability for these DNNs to work effectively in a wide range of scenarios, without retraining, paves the way for their widespread usage in analysing NMR data.



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[NMR paper] Investigation of protein-ligand complexes by ligand-based NMR methods
Apr 18, 2021 - 11:34 AM - by nmrlearner
nmrlearner's Avatar Investigation of protein-ligand complexes by ligand-based NMR methods

Molecular recognition is at the base of all biological events and its knowledge at atomic level is pivotal in the development of new drug design approaches. NMR spectroscopy is one of the most widely used technique to detect and characterize transient ligand-receptor interactions in solution. In particular, ligand-based NMR approaches, including NOE-based NMR techniques, diffusion experiments and relaxation methods, are excellent tools to investigate how ligands interact with their receptors....

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0 Replies | 14 Views
Researchers probe intriguing interaction between sugars and the SARS-CoV-2 spike protein - News-Medical.Net
Apr 17, 2021 - 1:47 AM - by nmrlearner
nmrlearner's Avatar Researchers probe intriguing interaction between sugars and the SARS-CoV-2 spike protein - News-Medical.Net

Researchers probe intriguing interaction between sugars and the SARS-CoV-2 spike protein News-Medical.Net Read here
0 Replies | 8 Views
[NMR paper] Expression, Purification, and Solution-State NMR Analysis of the Two Human Single-Stranded DNA-Binding Proteins hSSB1 (NABP2/OBFC2B) and hSSB2 (NAPB1/OBFC2A)
Apr 16, 2021 - 12:40 AM - by nmrlearner
nmrlearner's Avatar Expression, Purification, and Solution-State NMR Analysis of the Two Human Single-Stranded DNA-Binding Proteins hSSB1 (NABP2/OBFC2B) and hSSB2 (NAPB1/OBFC2A)

Single-stranded DNA-binding proteins (SSBs) are essential to all living organisms as protectors and guardians of the genome. Apart from the well-characterized RPA, humans have also evolved two further SSBs, termed hSSB1 and hSSB2. Over the last few years, we have used NMR spectroscopy to determine the molecular and structural details of both hSSBs and their interactions with DNA and RNA. Here we provide a detailed overview of how to express and purify recombinant versions of these important...

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0 Replies | 26 Views
[NMR paper] Binding Sites for Oligosaccharide Repeats from Lactic Acid Bacteria Exopolysaccharides on Bovine beta-Lactoglobulin Identified by NMR Spectroscopy
Apr 16, 2021 - 12:40 AM - by nmrlearner
nmrlearner's Avatar Binding Sites for Oligosaccharide Repeats from Lactic Acid Bacteria Exopolysaccharides on Bovine beta-Lactoglobulin Identified by NMR Spectroscopy

Lactic acid bacterial exopolysaccharides (EPS) are used in the food industry to improve the stability and rheological properties of fermented dairy products. ?-Lactoglobulin (BLG), the dominant whey protein in bovine milk, is well known to bind small molecules such as fatty acids, vitamins, and flavors, and to interact with neutral and anionic polysaccharides used in food and pharmaceuticals. While sparse data are available on the affinity of EPS-milk protein interactions, structural information...

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0 Replies | 10 Views
[NMR paper] A mixing microfluidic chip for real-time NMR monitoring of macromolecular reaction
Apr 16, 2021 - 12:40 AM - by nmrlearner
nmrlearner's Avatar A mixing microfluidic chip for real-time NMR monitoring of macromolecular reaction

NMR spectroscopy permits real-time monitoring of reactions that involve changes in the spectra of reactants. MICCS (MIcro Channeled Cell for Synthesis monitoring) is a microfluidic chip for such purposes, which is used to rapidly activate reactions by mixing the reactant solutions in the chip inserted into the typical NMR tube. Although it allows monitoring of chemical reactions of small compounds, its simple mixing system dependent on diffusion in the microchannel was not suitable for...

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0 Replies | 9 Views
A COVID moonshot: assessment of ligand binding to the SARS-CoV-2 main protease by saturation transfer difference NMR spectroscopy
Apr 15, 2021 - 12:12 PM - by nmrlearner
nmrlearner's Avatar A COVID moonshot: assessment of ligand binding to the SARS-CoV-2 main protease by saturation transfer difference NMR spectroscopy

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological cause of the coronavirus disease 2019, for which no effective antiviral therapeutics are available. The SARS-CoV-2 main protease (Mpro) is essential for viral replication and constitutes a promising therapeutic target. Many efforts aimed at deriving effective Mpro inhibitors are currently underway, including an international open-science discovery project, codenamed COVID Moonshot. As part of COVID Moonshot, we used saturation transfer difference nuclear magnetic resonance (STD-NMR) spectroscopy to assess the binding of putative Mpro ligands to the viral protease, including molecules identified by crystallographic fragment screening and novel compounds designed as Mpro inhibitors. In this manner, we aimed to complement enzymatic activity assays of Mpro performed by other groups with information on ligand affinity. We have made the Mpro STD-NMR data publicly available. Here, we provide detailed information on the NMR protocols used and challenges faced, thereby placing these data into context. Our goal is to assist the interpretation of Mpro STD-NMR data, thereby accelerating ongoing drug design efforts.



Source: Journal of Biomolecular NMR
0 Replies | 18 Views
Protein Crystallization and Crystallography Market Worth $1.7 billion Increasing Focus on Miniaturization interpreted by a new report - WhaTech
Apr 14, 2021 - 7:12 AM - by nmrlearner
nmrlearner's Avatar Protein Crystallization and Crystallography Market Worth $1.7 billion Increasing Focus on Miniaturization interpreted by a new report - WhaTech

Protein Crystallization and Crystallography Market Worth $1.7 billion Increasing Focus on Miniaturization interpreted by a new report WhaTech Read here
0 Replies | 13 Views
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