NMR paper Application of Dirichlet process mixture model to the identification of spin systems in protein NMR spectra.

		BioNMR > Educational resources > Journal club
[NMR paper] Application of Dirichlet process mixture model to the identification of spin systems in protein NMR spectra.

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

05-20-2018, 06:02 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

Application of Dirichlet process mixture model to the identification of spin systems in protein NMR spectra.

Application of Dirichlet process mixture model to the identification of spin systems in protein NMR spectra.

Related Articles Application of Dirichlet process mixture model to the identification of spin systems in protein NMR spectra.

J Biomol NMR. 2018 May 18;:

Authors: Klukowski P, Augoff M, Zamorski M, Gonczarek A, Walczak MJ

Abstract
Analysis of structure, function and interactions of proteins by NMR spectroscopy usually requires the assignment of resonances to the corresponding nuclei in protein. This task, although automated by methods such as FLYA or PINE, is still frequently performed manually. To facilitate the manual sequence-specific chemical shift assignment of complex proteins, we propose a method based on Dirichlet process mixture model (DPMM) that performs automated matching of groups of signals observed in NMR spectra to corresponding nuclei in protein sequence. The model has been extensively tested on 80 proteins retrieved from the BMRB database and has shown superior performance to the reference method.

PMID: 29777498 [PubMed - as supplied by publisher]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Application of Dirichlet process mixture model to the identification of spin systems in protein NMR spectra Application of Dirichlet process mixture model to the identification of spin systems in protein NMR spectra Abstract Analysis of structure, function and interactions of proteins by NMR spectroscopy usually requires the assignment of resonances to the corresponding nuclei in protein. This task, although automated by methods such as FLYA or PINE, is still frequently performed manually. To facilitate the manual sequence-specific chemical shift assignment of complex proteins, we propose a method based on Dirichlet process mixture model (DPMM) that...	nmrlearner	Journal club	0	05-19-2018 05:30 AM
A Model Sea Urchin Spicule Matrix Protein, rSpSM50,Is a Hydrogelator That Modifies and Organizes the Mineralization Process A Model Sea Urchin Spicule Matrix Protein, rSpSM50,Is a Hydrogelator That Modifies and Organizes the Mineralization Process http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.7b00083/20170511/images/medium/bi-2017-000833_0010.gif Biochemistry DOI: 10.1021/acs.biochem.7b00083 http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/PrIE9Gh7UCw More...	nmrlearner	Journal club	0	05-12-2017 02:14 AM
[NMR paper] The proteolysis process in fermented sausage model systems as studied by nmr relaxometry. THE PROTEOLYSIS PROCESS IN FERMENTED SAUSAGE MODEL SYSTEMS AS STUDIED BY NMR RELAXOMETRY. Related Articles THE PROTEOLYSIS PROCESS IN FERMENTED SAUSAGE MODEL SYSTEMS AS STUDIED BY NMR RELAXOMETRY. J Agric Food Chem. 2015 Mar 9; Authors: Garcia AB, Larsen LB, Cambero MI, Diaz KP, Bertram HC Abstract Proton NMR relaxation analyses were performed in sausage model systems (SMS) at different manufacturing times (0, 1, 3, 5, 7 and 9 days) to evaluate changes in water distribution and mobility. Three different water populations were...	nmrlearner	Journal club	0	03-10-2015 07:22 PM
Using CEM Process Control Systems for Moisture, Fat and Protein Analysis in ... - Azom.com Using CEM Process Control Systems for Moisture, Fat and Protein Analysis in ... - Azom.com http://www.bionmr.com//t1.gstatic.com/images?q=tbn:ANd9GcTss7wO5oxnTSZZmUl-Ar6LVL2ybAD0IymnVqJ4jkgzudHCCMjQORIiapM0Fg3p60HNec2u3RdN Azom.com <img alt="" height="1" width="1" /> Using CEM Process Control Systems for Moisture, Fat and Protein Analysis in ... Azom.com It combines a sophisticated NMR magnet for fat analysis with the SMART Turbo Microwave for solid and moisture analysis of in-process products, incoming raw meat, and finished goods. More precise than FTNIR and NIR systems, the MEAT...	nmrlearner	Online News	0	10-21-2014 03:56 AM
[NMR paper] Heteronuclear Transverse and Longitudinal Relaxation in AX4 Spin Systems: Application to 15N Relaxations in 15NH4+ Heteronuclear Transverse and Longitudinal Relaxation in AX4 Spin Systems: Application to 15N Relaxations in 15NH4+ Publication date: Available online 28 June 2014 Source:Journal of Magnetic Resonance</br> Author(s): Nicolas D. Werbeck , D. Flemming Hansen</br> The equations that describe the time-evolution of transverse and longitudinal 15N magnetisations in tetrahedral ammonium ions, 15NH4 +, are derived from the Bloch-Wangsness-Redfield density operator relaxation theory. It is assumed that the relaxation of the spin-states is dominated by (1) the intra-molecular...	nmrlearner	Journal club	0	06-29-2014 02:00 AM
Fast and accurate algorithm for the simulation of NMR spectra of large spin systems. Fast and accurate algorithm for the simulation of NMR spectra of large spin systems. Fast and accurate algorithm for the simulation of NMR spectra of large spin systems. J Magn Reson. 2011 Apr;209(2):123-30 Authors: Castillo AM, Patiny L, Wist J The computational cost for the simulation of NMR spectra grows exponentially with the number of nuclei. Today, the memory available to store the Hamiltonian limits the size of the system that can be studied. Modern computers enable to tackle systems containing up to 13 spins , which obviously does not...	nmrlearner	Journal club	0	07-23-2011 08:54 AM
Continuous-wave EPR at 275 GHz: Application to high-spin Fe3+ systems Continuous-wave EPR at 275 GHz: Application to high-spin Fe3+ systems Publication year: 2011 Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 11 March 2011</br> G., Mathies , H., Blok , J.A.J.M., Disselhorst , P., Gast , H., van der Meer , ...</br> The 275 GHz electron-paramagnetic-resonance spectrometer we reported on in 2004 has been equipped with a new probe head, which contains a cavity especially designed for operation in continuous-wave mode. The sensitivity and signal stability that is achieved with this new probe head is illustrated...	nmrlearner	Journal club	0	03-12-2011 05:21 PM

« 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