Automatic structure-based NMR methyl resonance assignment in large proteins - Nature.com

		BioNMR > NMR community > Online News
Automatic structure-based NMR methyl resonance assignment in large proteins - Nature.com

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

12-28-2023, 10:50 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,732

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

Automatic structure-based NMR methyl resonance assignment in large proteins - Nature.com

Automatic structure-based NMR methyl resonance assignment in large proteins - Nature.com

Automatic structure-based NMR methyl resonance assignment in large proteins Nature.com Read here

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Backbone-independent NMR resonance assignments of methyl probes in large proteins. Backbone-independent NMR resonance assignments of methyl probes in large proteins. Related Articles Backbone-independent NMR resonance assignments of methyl probes in large proteins. Nat Commun. 2021 Jan 29;12(1):691 Authors: Nerli S, De Paula VS, McShan AC, Sgourakis NG Abstract Methyl-specific isotope labeling is a powerful tool to study the structure, dynamics and interactions of large proteins and protein complexes by solution-state NMR. However, widespread applications of this methodology have been limited by challenges in...	nmrlearner	Journal club	0	01-31-2021 02:47 PM
[ASAP] Methyl-Based NMR Spectroscopy Methods for Uncovering Structural Dynamics in Large Proteins and Protein Complexes Methyl-Based NMR Spectroscopy Methods for Uncovering Structural Dynamics in Large Proteins and Protein Complexes https://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.8b00953/20181026/images/medium/bi-2018-00953s_0006.gif Biochemistry DOI: 10.1021/acs.biochem.8b00953 http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/VOv8DrY-3do More...	nmrlearner	Journal club	0	11-25-2018 06:02 AM
Automatic methyl assignment in large proteins by the MAGIC algorithm Automatic methyl assignment in large proteins by the MAGIC algorithm Abstract Selective methyl labeling is an extremely powerful approach to study the structure, dynamics and function of biomolecules by NMR. Despite spectacular progress in the field, such studies remain rather limited in number. One of the main obstacles remains the assignment of the methyl resonances, which is labor intensive and error prone. Typically, NOESY crosspeak patterns are manually correlated to the available crystal structure or an in silico template model of the protein....	nmrlearner	Journal club	0	11-03-2017 04:15 AM
[NMR paper] Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory. Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory. Related Articles Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory. J Am Chem Soc. 2017 Jul 10;: Authors: Pritišanac I, Degiacomi MT, Alderson TR, Carneiro MG, Ab E, Siegal G, Baldwin AJ Abstract Methyl groups are powerful probes for the analysis of structure, dynamics and function of supramolecular assemblies, using both solution- and solid-state NMR. Widespread application of the methodology has been...	nmrlearner	Journal club	0	07-12-2017 12:48 AM
Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory Iva Pritis?anac, Matteo T. Degiacomi, T. Reid Alderson, Marta G. Carneiro, Eiso AB, Gregg Siegal and Andrew J. Baldwin http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/jacs.6b11358/20170710/images/medium/ja-2016-11358e_0008.gif Journal of the American Chemical Society DOI: 10.1021/jacs.6b11358 http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/VuC8AlNsrfs	nmrlearner	Journal club	0	07-11-2017 09:20 AM
Amino acid recognition for automatic resonance assignment of intrinsically disordered proteins Amino acid recognition for automatic resonance assignment of intrinsically disordered proteins Abstract Resonance assignment is a prerequisite for almost any NMR-based study of proteins. It can be very challenging in some cases, however, due to the nature of the protein under investigation. This is the case with intrinsically disordered proteins, for example, whose NMR spectra suffer from low chemical shifts dispersion and generally low resolution. For these systems, sequence specific assignment is highly time-consuming, so the prospect of using...	nmrlearner	Journal club	0	02-19-2016 08:39 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
SAGA: rapid automatic mainchain NMR assignment for large proteins Abstract Here we describe a new algorithm for automatically determining the mainchain sequential assignment of NMR spectra for proteins. Using only the customary triple resonance experiments, assignments can be quickly found for not only small proteins having rather complete data, but also for large proteins, even when only half the residues can be assigned. The result of the calculation is not the single best assignment according to some criterion, but rather a large number of satisfactory assignments that are summarized in such a way as to help the user identify portions of the sequence...	nmrlearner	Journal club	0	08-14-2010 04:19 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