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

Go Back   BioNMR > Software > Molecular modeling software > NMR structure calculation
Advanced Search



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 Rating: Thread Rating: 1 votes, 5.00 average. Display Modes
  #1  
Unread 03-10-2005, 06:57 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 17,369
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

Link to PSSI program

Reference and abstract:

Probability-based protein secondary structure identification using combined NMR chemical-shift data.

Wang Y, Jardetzky O.

Division of Chemical Biology, Department of Molecular Pharmacology, Stanford University, Stanford, California 94305, USA.

Protein Sci. 2002 Apr;11(4):852-61.

For a long time, NMR chemical shifts have been used to identify protein secondary structures. Currently, this is accomplished through comparing the observed (1)H(alpha), (13)C(alpha), (13)C(beta), or (13)C' chemical shifts with the random coil values. Here, we present a new protocol, which is based on the joint probability of each of the three secondary structural types (beta-strand, alpha-helix, and random coil) derived from chemical-shift data, to identify the secondary structure. In combination with empirical smooth filters/functions, this protocol shows significant improvements in the accuracy and the confidence of identification. Updated chemical-shift statistics are reported, on the basis of which the reliability of using chemical shift to identify protein secondary structure is evaluated for each nucleus. The reliability varies greatly among the 20 amino acids, but, on average, is in the order of: (13)C(alpha)>(13)C'>(1)H(alpha)>(13)C(beta)>(15)N>(1)H(N) to distinguish an alpha-helix from a random coil; and (1)H(alpha)>(13)C(beta) >(1)H(N) approximately (13)C(alpha) approximately (13)C' approximately (15)N for a beta-strand from a random coil. Amide (15)N and (1)H(N) chemical shifts, which are generally excluded from the application, in fact, were found to be helpful in distinguishing a beta-strand from a random coil. In addition, the chemical-shift statistical data are compared with those reported previously, and the results are discussed. A JAVA User Interface program has been developed to make the entire procedure fully automated and is available via http://ccsr3150-p3.stanford.edu.
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Uncovering symmetry-breaking vector and reliability order for assigning secondary structures of proteins from atomic NMR chemical shifts in amino acids
Uncovering symmetry-breaking vector and reliability order for assigning secondary structures of proteins from atomic NMR chemical shifts in amino acids Abstract Unravelling the complex correlation between chemical shifts of 13 C α, 13 C β, 13 C?, 1 H α, 15 N, 1 H N atoms in amino acids of proteins from NMR experiment and local structural environments of amino acids facilitates the assignment of secondary structures of proteins. This is an important impetus for both determining the three-dimensional structure and understanding the biological function of proteins. The previous...
nmrlearner Journal club 0 11-14-2011 08:45 AM
Structure-based prediction of methyl chemical shifts in proteins
Structure-based prediction of methyl chemical shifts in proteins Abstract Protein methyl groups have recently been the subject of much attention in NMR spectroscopy because of the opportunities that they provide to obtain information about the structure and dynamics of proteins and protein complexes. With the advent of selective labeling schemes, methyl groups are particularly interesting in the context of chemical shift based protein structure determination, an approach that to date has exploited primarily the mapping between protein structures and backbone chemical shifts. In order to...
nmrlearner Journal club 0 07-15-2011 09:10 PM
[NMR paper] Secondary structural effects on protein NMR chemical shifts.
Secondary structural effects on protein NMR chemical shifts. Related Articles Secondary structural effects on protein NMR chemical shifts. J Biomol NMR. 2004 Nov;30(3):233-44 Authors: Wang Y For an amino acid in protein, its chemical shift, delta(phi, psi)(s), is expressed as a function of its backbone torsion angles (phi and psi) and secondary state (s): delta(phi, psi)(s=deltaphi, psi)_coil+Deltadelta(phi, psi)_s), where delta(phi, psi)(coil) represents its chemical shift at coil state (s=coil); Delta delta(phi, psi)(s) (s=sheet or helix) is...
nmrlearner Journal club 0 11-24-2010 10:03 PM
[NMR paper] The NMR solution structure and characterization of pH dependent chemical shifts of th
The NMR solution structure and characterization of pH dependent chemical shifts of the beta-elicitin, cryptogein. Related Articles The NMR solution structure and characterization of pH dependent chemical shifts of the beta-elicitin, cryptogein. J Biomol NMR. 1998 Nov;12(4):523-34 Authors: Gooley PR, Keniry MA, Dimitrov RA, Marsh DE, Keizer DW, Gayler KR, Grant BR The NMR structure of the 98 residue beta-elicitin, cryptogein, which induces a defence response in tobacco, was determined using 15N and 13C/15N labelled protein samples. In aqueous...
nmrlearner Journal club 0 11-17-2010 11:15 PM
[NMR paper] NMR chemical shifts and structure refinement in proteins.
NMR chemical shifts and structure refinement in proteins. Related Articles NMR chemical shifts and structure refinement in proteins. J Biomol NMR. 1993 Sep;3(5):607-12 Authors: Laws DD, de Dios AC, Oldfield E Computation of the 13C alpha chemical shifts (or shieldings) of glycine, alanine and valine residues in bovine and Drosophila calmodulins and Staphylococcal nuclease, and comparison with experimental values, is reported using a gauge-including atomic orbital quantum-chemical approach. The full approximately 24 ppm shielding range is...
nmrlearner Journal club 0 08-22-2010 03:01 AM
[NMR paper] Secondary and tertiary structural effects on protein NMR chemical shifts: an ab initi
Secondary and tertiary structural effects on protein NMR chemical shifts: an ab initio approach. Related Articles Secondary and tertiary structural effects on protein NMR chemical shifts: an ab initio approach. Science. 1993 Jun 4;260(5113):1491-6 Authors: de Dios AC, Pearson JG, Oldfield E Recent theoretical developments permit the prediction of 1H, 13C, 15N, and 19F nuclear magnetic resonance chemical shifts in proteins and offer new ways of analyzing secondary and tertiary structure as well as for probing protein electrostatics. For 13C,...
nmrlearner Journal club 0 08-21-2010 11:53 PM
The predictive accuracy of secondary chemical shifts is more affected by protein seco
Abstract Biomolecular NMR spectroscopy frequently employs estimates of protein secondary structure using secondary chemical shift (?δ) values, measured as the difference between experimental and random coil chemical shifts (RCCS). Most published random coil data have been determined in aqueous conditions, reasonable for non-membrane proteins, but potentially less relevant for membrane proteins. Two new RCCS sets are presented here, determined in dimethyl sulfoxide (DMSO) and chloroform:methanol:water (4:4:1 by volume) at 298 K. A web-based program, CS-CHEMeleon, has been implemented to...
nmrlearner Journal club 0 08-14-2010 04:19 AM
Computational prediction of three-dimensional protein structure from NMR chemical shifts - Kai Kohlhoff
Computational prediction of three-dimensional protein structure from NMR chemical shifts - Kai Kohlhoff, Microsoft Research Summer School , Cambridge , July 2008
MCGowan Educational web pages 0 09-16-2008 02:10 AM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This 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



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



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2017, 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 08:46 PM.


Map