ncIDP-assign: A SPARKY extension for the effective NMR assignment of intrinsically disordered proteins.

		BioNMR > Educational resources > Journal club
ncIDP-assign: A SPARKY extension for the effective NMR assignment of intrinsically disordered proteins.

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

03-05-2011, 01:02 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

ncIDP-assign: A SPARKY extension for the effective NMR assignment of intrinsically disordered proteins.

ncIDP-assign: A SPARKY extension for the effective NMR assignment of intrinsically disordered proteins.

ncIDP-assign: A SPARKY extension for the effective NMR assignment of intrinsically disordered proteins.

Bioinformatics. 2011 Mar 3;

Authors: Tamiola K, Mulder FA

SUMMARY: We describe here the ncIDP-assign extension for the popular NMR assignment programme SPARKY, which aids in the sequence-specific resonance assignment of intrinsically disordered proteins (IDPs). The assignment plugin greatly facilitates the effective matching of a set of connected resonances to the correct position in the sequence by making use of IDP random coil chemical shifts. AVAILABILITY: The ncIDP-assign extension is available at www.proteinnmr.org/. CONTACT: Bug reports, questions or comments should be sent to: support@protein-nmr.org.

PMID: 21372082 [PubMed - as supplied by publisher]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins Abstract Four novel 5D (HACA(N)CONH, HNCOCACB, (HACA)CON(CA)CONH, (H)NCO(NCA)CONH), and one 6D ((H)NCO(N)CACONH) NMR pulse sequences are proposed. The new experiments employ non-uniform sampling that enables achieving high resolution in indirectly detected dimensions. The experiments facilitate resonance assignment of intrinsically disordered proteins. The novel pulse sequences were successfully tested using Î´ subunit (20 kDa) of Bacillus subtilis RNA polymerase...	nmrlearner	Journal club	0	02-21-2012 03:40 AM
Paramagnetic relaxation enhancement to improve sensitivity of fast NMR methods: application to intrinsically disordered proteins Paramagnetic relaxation enhancement to improve sensitivity of fast NMR methods: application to intrinsically disordered proteins Abstract We report enhanced sensitivity NMR measurements of intrinsically disordered proteins in the presence of paramagnetic relaxation enhancement (PRE) agents such as Ni2+-chelated DO2A. In proton-detected 1H-15N SOFAST-HMQC and carbon-detected (H-flip)13CO-15N experiments, faster longitudinal relaxation enables the usage of even shorter interscan delays. This results in higher NMR signal intensities per units of experimental time, without adverse line...	nmrlearner	Journal club	0	10-21-2011 10:04 PM
Covalent structural changes in unfolded GroES that lead to amyloid fibril formation detected by NMR: Insight into intrinsically disordered proteins. Covalent structural changes in unfolded GroES that lead to amyloid fibril formation detected by NMR: Insight into intrinsically disordered proteins. Covalent structural changes in unfolded GroES that lead to amyloid fibril formation detected by NMR: Insight into intrinsically disordered proteins. J Biol Chem. 2011 Apr 20; Authors: Iwasa H, Meshitsuka S, Hongo K, Mizobata T, Kawata Y Co-chaperonin GroES from E. coli works with chaperonin GroEL to mediate the folding reactions of various proteins. However, under specific conditions, i. e., the...	nmrlearner	Journal club	0	04-22-2011 02:00 PM
Extension of the HA-detection based approach: (HCA)CON(CA)H and (HCA)NCO(CA)H experiments for the main-chain assignment of intrinsically disordered proteins Extension of the HA-detection based approach: (HCA)CON(CA)H and (HCA)NCO(CA)H experiments for the main-chain assignment of intrinsically disordered proteins Abstract Extensive resonance overlap exacerbates assignment of intrinsically disordered proteins (IDPs). This issue can be circumvented by utilizing 15N, 13Câ?² and 1HN spins, where the chemical shift dispersion is mainly dictated by the characteristics of consecutive amino acid residues. Especially 15N and 13Câ?² spins offer superior chemical shift dispersion in comparison to 13CÎ± and 13CÎ² spins. However, HN-detected experiments...	nmrlearner	Journal club	0	01-29-2011 05:31 AM
Random coil chemical shift for intrinsically disordered proteins: effects of temperature and pH Random coil chemical shift for intrinsically disordered proteins: effects of temperature and pH Abstract Secondary chemical shift analysis is the main NMR method for detection of transiently formed secondary structure in intrinsically disordered proteins. The quality of the secondary chemical shifts is dependent on an appropriate choice of random coil chemical shifts. We report random coil chemical shifts and sequence correction factors determined for a GGXGG peptide series following the approach of Schwarzinger et al. (J Am Chem Soc 123(13):2970â??2978, 2001). The chemical shifts are...	nmrlearner	Journal club	0	01-17-2011 02:40 AM
Strategy for complete NMR assignment of disordered proteins with highly repetitive se Strategy for complete NMR assignment of disordered proteins with highly repetitive sequences based on resolution-enhanced 5D experiments Abstract A strategy for complete backbone and side-chain resonance assignment of disordered proteins with highly repetitive sequence is presented. The protocol is based on three resolution-enhanced NMR experiments: 5D HN(CA)CONH provides sequential connectivity, 5D HabCabCONH is utilized to identify amino acid types, and 5D HC(CC-TOCSY)CONH is used to assign the side-chain resonances. The improved resolution was achieved by a combination of high...	nmrlearner	Journal club	0	10-06-2010 02:16 AM
Strategy for complete NMR assignment of disordered proteins with highly repetitive se Strategy for complete NMR assignment of disordered proteins with highly repetitive sequences based on resolution-enhanced 5D experiments. Strategy for complete NMR assignment of disordered proteins with highly repetitive sequences based on resolution-enhanced 5D experiments. J Biomol NMR. 2010 Oct 2; Authors: MotÃ¡Ä?kovÃ¡ V, NovÃ¡Ä?ek J, Zawadzka-Kazimierczuk A, Kazimierczuk K, ZÃ*dek L, SanderovÃ¡ H, KrÃ¡snÃ½ L, KoÅºmiÅ?ski W, SklenÃ¡Å? V A strategy for complete backbone and side-chain resonance assignment of disordered proteins with highly...	nmrlearner	Journal club	0	10-05-2010 12:11 PM
HA-detected experiments for the backbone assignment of intrinsically disordered prote Abstract We propose a new alpha proton detection based approach for the sequential assignment of natively unfolded proteins. The proposed protocol superimposes on following features: HA-detection (1) enables assignment of natively unfolded proteins at any pH, i.e., it is not sensitive to rapid chemical exchange undergoing in natively unfolded proteins even at moderately high pH. (2) It allows straightforward assignment of proline-rich polypeptides without additional proline-customized experiments. (3) It offers more streamlined and less ambiguous assignment based on solely intraresidual...	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