NMR paper Experimental Protein Structure Verification by Scoring with a Single, Unassigned NMR Spectrum.

		BioNMR > Educational resources > Journal club
[NMR paper] Experimental Protein Structure Verification by Scoring with a Single, Unassigned NMR Spectrum.

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

09-15-2015, 11:12 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,776

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

Experimental Protein Structure Verification by Scoring with a Single, Unassigned NMR Spectrum.

Experimental Protein Structure Verification by Scoring with a Single, Unassigned NMR Spectrum.

Experimental Protein Structure Verification by Scoring with a Single, Unassigned NMR Spectrum.

Structure. 2015 Sep 9;

Authors: Courtney JM, Ye Q, Nesbitt AE, Tang M, Tuttle MD, Watt ED, Nuzzio KM, Sperling LJ, Comellas G, Peterson JR, Morrissey JH, Rienstra CM

Abstract
Standard methods for de novo protein structure determination by nuclear magnetic resonance (NMR) require time-consuming data collection and interpretation efforts. Here we present a qualitatively distinct and novel approach, called Comparative, Objective Measurement of Protein Architectures by Scoring Shifts (COMPASS), which identifies the best structures from a set of structural models by numerical comparison with a single, unassigned 2D (13)C-(13)C NMR spectrum containing backbone and side-chain aliphatic signals. COMPASS does not require resonance assignments. It is particularly well suited for interpretation of magic-angle spinning solid-state NMR spectra, but also applicable to solution NMR spectra. We demonstrate COMPASS with experimental data from four proteins-GB1, ubiquitin, DsbA, and the extracellular domain of human tissue factor-and with reconstructed spectra from 11 additional proteins. For all these proteins, with molecular mass up to 25*kDa, COMPASS distinguished the correct fold, most often within 1.5*Å root-mean-square deviation of the reference structure.

PMID: 26365800 [PubMed - as supplied by publisher]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Experimental Protein Structure Verification by Scoring with a Single, Unassigned NMR Spectrum Experimental Protein Structure Verification by Scoring with a Single, Unassigned NMR Spectrum Publication date: Available online 10 September 2015 Source:Structure</br> Author(s): JosephM. Courtney, Qing Ye, AnnaE. Nesbitt, Ming Tang, MarcusD. Tuttle, EricD. Watt, KristinM. Nuzzio, LindsayJ. Sperling, Gemma Comellas, JosephR. Peterson, JamesH. Morrissey, Chad*M. Rienstra</br> Standard methods for de novo protein structure determination by nuclear magnetic resonance (NMR) require time-consuming data collection and interpretation...	nmrlearner	Journal club	0	09-11-2015 06:48 AM
[NMR paper] Protein residue linking in a single spectrum for magic-angle spinning NMR assignment. Protein residue linking in a single spectrum for magic-angle spinning NMR assignment. Protein residue linking in a single spectrum for magic-angle spinning NMR assignment. J Biomol NMR. 2015 Jun 16; Authors: Andreas LB, Stanek J, Le Marchand T, Bertarello A, Paepe DC, Lalli D, Krej?íková M, Doyen C, Öster C, Knott B, Wegner S, Engelke F, Felli IC, Pierattelli R, Dixon NE, Emsley L, Herrmann T, Pintacuda G Abstract Here we introduce a new pulse sequence for resonance assignment that halves the number of data sets required...	nmrlearner	Journal club	0	06-17-2015 09:27 PM
Protein residue linking in a single spectrum for magic-angle spinning NMR assignment Protein residue linking in a single spectrum for magic-angle spinning NMR assignment Abstract Here we introduce a new pulse sequence for resonance assignment that halves the number of data sets required for sequential linking by directly correlating sequential amide resonances in a single diagonal-free spectrum. The method is demonstrated with both microcrystalline and sedimented deuterated proteins spinning at 60 and 111ÂkHz, and a fully protonated microcrystalline protein spinning at 111ÂkHz, with as little as 0.5Â*mg protein sample. We...	nmrlearner	Journal club	0	06-16-2015 04:27 AM
[Stan NMR blog] Automatic Structure Verification (ASV) Automatic Structure Verification (ASV) John Hollerton's reflection about the feasibility of ASV software and its usefulness Source: Stan blog library	nmrlearner	News from NMR blogs	0	03-26-2012 07:34 PM
[Ryan's blog] Are We There Yet? Automated Structure Verification (ASV) Source: Ryan's blog Are We There Yet? Automated Structure Verification (ASV) When I created this blog several years ago, one of the first links I added to my blog was to Stan's NMR Blog. Over the years I have had the pleasure to meet Stan who is a wonderful individual. His... Read more...	nmrlearner	News from NMR blogs	0	05-19-2011 09:02 PM
[Stan NMR blog] Automatic Structure Verification (ASV) Automatic Structure Verification (ASV) John Hollerton's reflection about the feasibility of ASV software and its usefulness Source: Stan blog library	nmrlearner	News from NMR blogs	0	04-17-2011 02:33 PM
[NMR paper] Assignment of the 1H NMR spectrum and secondary structure elucidation of the single-s Assignment of the 1H NMR spectrum and secondary structure elucidation of the single-stranded DNA binding protein encoded by the filamentous bacteriophage IKe. Related Articles Assignment of the 1H NMR spectrum and secondary structure elucidation of the single-stranded DNA binding protein encoded by the filamentous bacteriophage IKe. Biochemistry. 1992 Feb 4;31(4):1254-62 Authors: van Duynhoven JP, Folkers PJ, Prinse CW, Harmsen BJ, Konings RN, Hilbers CW By means of 2D NMR techniques, all backbone resonances in the 1H NMR spectrum of the...	nmrlearner	Journal club	0	08-21-2010 11:41 PM
[Ryan's blog] A Case for more NMR, and maybe even Automated Structure Verification? Source: Ryan's blog A Case for more NMR, and maybe even Automated Structure Verification? I've spent a lot of time over the past couple of years visiting both scientists and directors in Pharma and having discussions around the concept of automated structure verification, whether or not there is enough characterization being done on screens,...	nmrlearner	News from NMR blogs	0	08-21-2010 08:57 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