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

Go Back   BioNMR > Software > NMR software
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 07-18-2006, 09:03 PM
Junior Member
 
Join Date: Jul 2006
Posts: 2
Points: 14, Level: 1
Points: 14, Level: 1 Points: 14, Level: 1 Points: 14, Level: 1
Level up: 27%, 36 Points needed
Level up: 27% Level up: 27% Level up: 27%
Activity: 0%
Activity: 0% Activity: 0% Activity: 0%
NMR Credits: 0
NMR Points: 14
Downloads: 0
Uploads: 0
Default

Please check this program and let me know if it does work for your random coil peptides.

http://bloch.anu.edu.au/cgi-bin/shiftpred/shiftpred.cgi

Thank you,
Bogdan Bancia
bbancia@yahoo.com

Reply With Quote


Did you find this post helpful? Yes | No

  #2  
Old 03-30-2007, 02:48 PM
premprakash's Avatar
Junior Member
 
Join Date: Mar 2007
Posts: 7
Points: 24, Level: 1
Points: 24, Level: 1 Points: 24, Level: 1 Points: 24, Level: 1
Level up: 47%, 26 Points needed
Level up: 47% Level up: 47% Level up: 47%
Activity: 0%
Activity: 0% Activity: 0% Activity: 0%
NMR Credits: 0
NMR Points: 24
Downloads: 0
Uploads: 0
Default Re:

Hi! have posted a program which predict the chemical sift of random coil by submitting the one letter code sequence of protein.
Are you working on protein structure problem? I am working on solving the protein structure and have just started the work.
cheers!
Prem Prakash Pathak
Reply With Quote


Did you find this post helpful? Yes | No
  #3  
Old 04-13-2007, 03:54 PM
Junior Member
 
Join Date: Jul 2006
Posts: 2
Points: 14, Level: 1
Points: 14, Level: 1 Points: 14, Level: 1 Points: 14, Level: 1
Level up: 27%, 36 Points needed
Level up: 27% Level up: 27% Level up: 27%
Activity: 0%
Activity: 0% Activity: 0% Activity: 0%
NMR Credits: 0
NMR Points: 14
Downloads: 0
Uploads: 0
Default

Hi Prem,

I finished my work with proteins in June 2004 when I submited my MSc thesis at the Australian National University, in Canberra, Australia. Now I'm a teacher back home in Romania but still keeping an eye on the NMR stuff.
Hope the program is going to help you in your work!

Cheers,
Bogdan
Reply With Quote


Did you find this post helpful? Yes | No
Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
RCI - Random Coil Index for predicting protein flexibility from chemical shifts
RCI website RCI method predicts protein flexibility by calculating the Random Coil Index from backbone chemical shifts and predicting values of model-free order parameters as well as per-residue RMSF of NMR and MD ensembles from the Random Coil Index. The key advantages of this protocol over existing methods of studying protein flexibility are (i) it does not require prior knowledge of a protein's tertiary structure, (ii) it is not sensitive to the protein's overall tumbling and (iii) it does not require additional NMR measurements beyond the standard experiments for backbone...
markber NMR software 0 02-02-2012 11:36 PM
SHIFTX2: Chemical Shift Prediction
SHIFTX2 website SHIFTX2 is capable of rapidly and accurately calculating diamagnetic 1H, 13C and 15N chemical shifts from protein coordinate data. Compared to its predecessor (SHIFTX) and to other existing protein chemical shift prediction programs, SHIFTX2 is substantially more accurate (up to 26% better by correlation coefficient with an RMS error that is up to 3.3× smaller) than the next best performing program. It also provides significantly more coverage (up to 10% more), is significantly faster (up to 8.5×) and capable of calculating a wider variety of backbone and side chain...
gwnmr NMR software 0 01-10-2012 06:13 PM
Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution
Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution Abstract Random coil chemical shifts are necessary for secondary chemical shift analysis, which is the main NMR method for identification of secondary structure in proteins. One of the largest challenges in the determination of random coil chemical shifts is accounting for the effect of neighboring residues. The contributions from the neighboring residues are typically removed by using neighbor correction factors determined based on each...
nmrlearner Journal club 0 06-06-2011 12:53 AM
SHIFTX2: significantly improved protein chemical shift prediction
SHIFTX2: significantly improved protein chemical shift prediction Abstract A new computer program, called SHIFTX2, is described which is capable of rapidly and accurately calculating diamagnetic 1H, 13C and 15N chemical shifts from protein coordinate data. Compared to its predecessor (SHIFTX) and to other existing protein chemical shift prediction programs, SHIFTX2 is substantially more accurate (up to 26% better by correlation coefficient with an RMS error that is up to 3.3Ã? smaller) than the next best performing program. It also provides significantly more coverage (up to 10% more),...
nmrlearner Journal club 0 04-01-2011 09:31 PM
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
[NMR paper] Proline-directed random-coil chemical shift values as a tool for the NMR assignment o
Proline-directed random-coil chemical shift values as a tool for the NMR assignment of the tau phosphorylation sites. Related Articles Proline-directed random-coil chemical shift values as a tool for the NMR assignment of the tau phosphorylation sites. Chembiochem. 2004 Jan 3;5(1):73-8 Authors: Lippens G, Wieruszeski JM, Leroy A, Smet C, Sillen A, Buée L, Landrieu I NMR spectroscopy of the full-length neuronal Tau protein has proved to be difficult due to the length of the protein and the unfavorable amino acid composition. We show that the...
nmrlearner Journal club 0 11-24-2010 09:25 PM
[NMR paper] Sequence-dependent correction of random coil NMR chemical shifts.
Sequence-dependent correction of random coil NMR chemical shifts. Related Articles Sequence-dependent correction of random coil NMR chemical shifts. J Am Chem Soc. 2001 Apr 4;123(13):2970-8 Authors: Schwarzinger S, Kroon GJ, Foss TR, Chung J, Wright PE, Dyson HJ Random coil chemical shifts are commonly used to detect secondary structure elements in proteins in chemical shift index calculations. While this technique is very reliable for folded proteins, application to unfolded proteins reveals significant deviations from measured random coil...
nmrlearner Journal club 0 11-19-2010 08:32 PM
Protein secondary structure prediction using NMR chemical shift data.
Protein secondary structure prediction using NMR chemical shift data. Related Articles Protein secondary structure prediction using NMR chemical shift data. J Bioinform Comput Biol. 2010 Oct;8(5):867-84 Authors: Zhao Y, Alipanahi B, Li SC, Li M Accurate determination of protein secondary structure from the chemical shift information is a key step for NMR tertiary structure determination. Relatively few work has been done on this subject. There needs to be a systematic investigation of algorithms that are (a) robust for large datasets; (b)...
nmrlearner Journal club 0 10-29-2010 07:05 PM



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 09:08 PM.


Map