Protein NMR assignment by isotope pattern recognition - Science

		BioNMR > NMR community > Online News
Protein NMR assignment by isotope pattern recognition - Science

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

10-09-2024, 02:22 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,780

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

Protein NMR assignment by isotope pattern recognition - Science

Protein NMR assignment by isotope pattern recognition - Science

Protein NMR assignment by isotope pattern recognition Science Read here

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Time-optimized protein NMR assignment with an integrative deep ... - Science Time-optimized protein NMR assignment with an integrative deep ... - Science Time-optimized protein NMR assignment with an integrative deep ... Science Read here	nmrlearner	Online News	0	11-23-2023 10:09 AM
[NMR paper] NMR spectrum reconstruction as a pattern recognition problem NMR spectrum reconstruction as a pattern recognition problem No abstract More...	nmrlearner	Journal club	0	12-03-2022 10:25 PM
Partially-deuterated samples of HET-s(218â??289) fibrils: assignment and deuterium isotope effect Partially-deuterated samples of HET-s(218â??289) fibrils: assignment and deuterium isotope effect Abstract Fast magic-angle spinning and partial sample deuteration allows direct detection of 1H in solid-state NMR, yielding significant gains in mass sensitivity. In order to further analyze the spectra, 1H detection requires assignment of the 1H resonances. In this work, resonance assignments of backbone HN and HÎ± are presented for HET-s(218â??289) fibrils, based on the existing assignment of CÎ±, CÎ², Câ??, and N resonances. The samples used are...	nmrlearner	Journal club	0	01-11-2017 01:23 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
[NMR paper] Nano-Mole Scale Side-Chain Signal Assignment by 1H-Detected Protein Solid-State NMR by Ultra-Fast Magic-Angle Spinning and Stereo-Array Isotope Labeling. Nano-Mole Scale Side-Chain Signal Assignment by 1H-Detected Protein Solid-State NMR by Ultra-Fast Magic-Angle Spinning and Stereo-Array Isotope Labeling. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.plosone.org-images-pone_120x30.png Related Articles Nano-Mole Scale Side-Chain Signal Assignment by 1H-Detected Protein Solid-State NMR by Ultra-Fast Magic-Angle Spinning and Stereo-Array Isotope Labeling. PLoS One. 2015;10(4):e0122714 Authors: Wang S, Parthasarathy S, Nishiyama Y, Endo Y, Nemoto T, Yamauchi K, Asakura T,...	nmrlearner	Journal club	0	04-11-2015 12:04 AM
[NMR paper] [Application of ¹H-NMR-based pattern recognition in serum metabolomics of patients with chronic heart failure]. . Related Articles . Nan Fang Yi Ke Da Xue Xue Bao. 2012 Mar;32(3):415-9 Authors: Du ZY, Shen A, Su L, Liang JQ, Xu DL Abstract OBJECTIVE: To investigate the feasibility of applying (1)H-NMR-based pattern recognition in the studies of serum metabonomics in chronic heart failure (HF).	nmrlearner	Journal club	0	09-27-2013 05:26 PM
[NMR paper] A new strategy for sequential assignment of intrinsically unstructured proteins based on 15N single isotope labelling A new strategy for sequential assignment of intrinsically unstructured proteins based on 15N single isotope labelling Publication date: Available online 23 July 2013 Source:Journal of Magnetic Resonance</br> Author(s): Juan Lopez , Puneet Ahuja , Melanie Gérard , Jean Michel Wieruszeski , Guy Lippens</br> We describe a new efficient strategy for the sequential assignment of amide resonances of a conventional 15N-1H HSQC spectrum of intrinsically unfolded proteins, based on composite NOESY-TOCSY and TOCSY-NOESY mixing times. These composite mixing times lead to a...	nmrlearner	Journal club	0	07-23-2013 09:52 PM
[NMR paper] Use of graph theory for secondary structure recognition and sequential assignment in Use of graph theory for secondary structure recognition and sequential assignment in heteronuclear (13C, 15N) NMR spectra: application to HU protein from Bacillus stearothermophilus. Related Articles Use of graph theory for secondary structure recognition and sequential assignment in heteronuclear (13C, 15N) NMR spectra: application to HU protein from Bacillus stearothermophilus. Biopolymers. 1996 Nov;39(5):691-707 Authors: van Geerestein-Ujah EC, Mariani M, Vis H, Boelens R, Kaptein R A computer-assisted procedure, based upon a branch of...	nmrlearner	Journal club	0	08-22-2010 02:20 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