BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search
Home Forums Wiki NMR feeds Downloads Register Today's Posts



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
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:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
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:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
 
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Old 03-05-2011, 01:02 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,777
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default 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
Reply With Quote


Did you find this post helpful? Yes | No

Reply
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 δ 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, 13C� and 1HN spins, where the chemical shift dispersion is mainly dictated by the characteristics of consecutive amino acid residues. Especially 15N and 13C� spins offer superior chemical shift dispersion in comparison to 13Cα and 13Cβ 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: MotáÄ?ková V, NováÄ?ek J, Zawadzka-Kazimierczuk A, Kazimierczuk K, ZÃ*dek L, Sanderová H, Krásný L, KoźmiÅ?ski W, SklenáÅ? 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



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



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2024, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 08:13 AM.


Map