Deep Neural Networks for Methyl NMR Spectroscopy of Large Proteins - AZoOptics

		BioNMR > NMR community > Online News
Deep Neural Networks for Methyl NMR Spectroscopy of Large Proteins - AZoOptics

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

Torsion angles from chemical shifts:

Preditor

TALOS

Promega- Proline

Secondary structure from chemical shifts:

CSI (via RCI server)

TALOS

MICS caps, β-turns

d2D

PECAN

Flexibility from chemical shifts:

RCI

Interactions from chemical shifts:

HADDOCK

Chemical shifts re-referencing:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

Quality Control Check

NMR spectrum prediction:

FANDAS

MestReS

V-NMR

Flexibility from structure:

Backbone S2

Methyl S2

B-factor

Molecular dynamics:

Gromacs

Amber

Antechamber

Chemical shifts prediction:

From structure:

Shiftx2

Sparta+

Camshift

CH3shift- Methyl

ArShift- Aromatic

ShiftS

Proshift

PPM

CheShift-2- Cα

From sequence:

Shifty

Camcoil

Poulsen_rc_CS

Disordered proteins:

MAXOCC

Format conversion & validation:

CCPN

From NMR-STAR 3.1

Validate NMR-STAR 3.1

NMR sample preparation:

Protein disorder:

DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

Thread Tools

Search this Thread

Rate Thread

Display Modes

06-19-2024, 09:50 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

Deep Neural Networks for Methyl NMR Spectroscopy of Large Proteins - AZoOptics

Deep Neural Networks for Methyl NMR Spectroscopy of Large Proteins - AZoOptics

Deep Neural Networks for Methyl NMR Spectroscopy of Large Proteins AZoOptics Read here

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Solution-state methyl NMR spectroscopy of large non-deuterated proteins enabled by deep neural networks - Nature.com Solution-state methyl NMR spectroscopy of large non-deuterated proteins enabled by deep neural networks - Nature.com Solution-state methyl NMR spectroscopy of large non-deuterated proteins enabled by deep neural networks Nature.com Read here	nmrlearner	Online News	0	06-15-2024 04:21 PM
[NMR paper] Solution-state methyl NMR spectroscopy of large non-deuterated proteins enabled by deep neural networks Solution-state methyl NMR spectroscopy of large non-deuterated proteins enabled by deep neural networks Methyl-TROSY nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for characterising large biomolecules in solution. However, preparing samples for these experiments is demanding and entails deuteration, limiting its use. Here we demonstrate that NMR spectra recorded on protonated, uniformly ^(13)C labelled samples can be processed using deep neural networks to yield spectra that are of similar quality to typical deuterated methyl-TROSY spectra, potentially providing...	nmrlearner	Journal club	0	06-14-2024 04:20 PM
Towards autonomous analysis of chemical exchange saturation transfer experiments using deep neural networks Towards autonomous analysis of chemical exchange saturation transfer experiments using deep neural networks Abstract Macromolecules often exchange between functional states on timescales that can be accessed with NMR spectroscopy and many NMR tools have been developed to characterise the kinetics and thermodynamics of the exchange processes, as well as the structure of the conformers that are involved. However, analysis of the NMR data that report on exchanging macromolecules often hinges on complex least-squares fitting procedures as well as human...	nmrlearner	Journal club	0	05-29-2022 03:31 AM
[NMR paper] DEEP picker is a deep neural network for accurate deconvolution of complex two-dimensional NMR spectra DEEP picker is a deep neural network for accurate deconvolution of complex two-dimensional NMR spectra The analysis of nuclear magnetic resonance (NMR) spectra for the comprehensive and unambiguous identification and characterization of peaks is a difficult, but critically important step in all NMR analyses of complex biological molecular systems. Here, we introduce DEEP Picker, a deep neural network (DNN)-based approach for peak picking and spectral deconvolution which semi-automates the analysis of two-dimensional NMR spectra. DEEP Picker includes 8 hidden convolutional layers and was...	nmrlearner	Journal club	0	09-04-2021 10:34 AM
Students bring 'fresh insights' to scientific research on gene expression, deep neural networks and more - Clark University News Hub http://www.bionmr.com//t1.gstatic.com/images?q=tbn:ANd9GcTVd062HSNkufpFLOXoHxhOr1s0onXKhPyi91bbXm51srwsuet1eajYCvbuLO7yooXH_P0TNwUX Clark University News Hub <img alt="" height="1" width="1"> Students bring 'fresh insights' to scientific research on gene expression, deep neural networks and more Clark University News Hub ... biochemistry and molecular biology senior Pinky Htun '17 of Myanmar spent June and July isolating, purifying and studying proteins using state-of-the-art lab equipment, including a high-speed centrifuge and a nuclear magnetic resonance spectrometer. Students...	nmrlearner	Online News	0	08-25-2016 05:42 AM
Efficient Acquisition of High-Resolution 4-D Diagonal-Suppressed Methyl-Methyl NOESY for Large Proteins Efficient Acquisition of High-Resolution 4-D Diagonal-Suppressed Methyl-Methyl NOESY for Large Proteins Publication year: 2012 Source:Journal of Magnetic Resonance</br> Jie Wen, Jihui Wu, Pei Zhou</br> The methyl-methyl NOESYexperimentplays an important role in determiningthe global folds of large proteins. Despite the high sensitivity of this experiment, the analysisof methyl-methyl NOEs is frequently hindered by the limited chemical shift dispersion of methyl groups, particularly methyl protons. Thismakes it difficult to unambiguously assign all of the methyl-methyl...	nmrlearner	Journal club	0	03-10-2012 10:54 AM
[NMR paper] Application of neural networks to automated assignment of NMR spectra of proteins. Application of neural networks to automated assignment of NMR spectra of proteins. Related Articles Application of neural networks to automated assignment of NMR spectra of proteins. J Biomol NMR. 1994 Jan;4(1):35-46 Authors: Hare BJ, Prestegard JH Simulated neural networks are described which aid the assignment of protein NMR spectra. A network trained to recognize amino acid type from TOCSY data was trained on 148 assigned spin systems from E. coli acyl carrier proteins (ACPs) and tested on spin systems from spinach ACP, which has a 37%...	nmrlearner	Journal club	0	08-22-2010 03:33 AM
[NMR paper] Application of neural networks to automated assignment of NMR spectra of proteins. Application of neural networks to automated assignment of NMR spectra of proteins. Related Articles Application of neural networks to automated assignment of NMR spectra of proteins. J Biomol NMR. 1994 Jan;4(1):35-46 Authors: Hare BJ, Prestegard JH Simulated neural networks are described which aid the assignment of protein NMR spectra. A network trained to recognize amino acid type from TOCSY data was trained on 148 assigned spin systems from E. coli acyl carrier proteins (ACPs) and tested on spin systems from spinach ACP, which has a 37%...	nmrlearner	Journal club	0	08-22-2010 03:33 AM

« Previous Thread | Next Thread »

Posting Rules
You may not post new threads You may not post replies You may not post attachments You may not edit your posts BB code is On Smilies are On [IMG] code is On HTML code is On Trackbacks are Off Pingbacks are Off Refbacks are Off