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



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  
Unread 11-18-2010, 09:15 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 18,813
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 A tracked approach for automated NMR assignments in proteins (TATAPRO).

A tracked approach for automated NMR assignments in proteins (TATAPRO).

Related Articles A tracked approach for automated NMR assignments in proteins (TATAPRO).

J Biomol NMR. 2000 Jun;17(2):125-36

Authors: Atreya HS, Sahu SC, Chary KV, Govil G

A novel automated approach for the sequence specific NMR assignments of 1HN, 13Calpha, 13Cbeta, 13C'/1Halpha and 15N spins in proteins, using triple resonance experimental data, is presented. The algorithm, TATAPRO (Tracked AuTomated Assignments in Proteins) utilizes the protein primary sequence and peak lists from a set of triple resonance spectra which correlate 1HN and 15N chemical shifts with those of 13Calpha, 13Cbeta and 13C'/1Halpha. The information derived from such correlations is used to create a 'master-_list' consisting of all possible sets of 1HN(i), 15N(i)13Calpha(i),13Cbeta(i) 13C'beta(i)/1Halpha(i), 13Calpha(i-1), 13Cbeta(i-1) and 13C'(i-1)/1Halpha(i-1) chemical shifts. On the basis of an extensive statistical analysis of 13Calpha and 13Cbeta chemical shift data of proteins derived from the BioMagResBank (BMRB), it is shown that the 20 amino acid residues can be grouped into eight distinct categories, each of which is assigned a unique two-digit code. Such a code is used to tag individual sets of chemical shifts in the master_list and also to translate the protein primary sequence into an array called pps_array. The program then uses the master_list to search for neighbouring partners of a given amino acid residue along the polypeptide chain and sequentially assigns a maximum possible stretch of residues on either side. While doing so. each assigned residue is tracked in an array called assig_array, with the two-digit code assigned earlier. The assig_array is then mapped onto the pps_array for sequence specific resonance assignment. The program has been tested using experimental data on a calcium binding protein from Entamoeba histolytica (Eh-CaBP, 15 kDa) having substantial internal sequence homology and using published data on four other proteins in the molecular weight range of 18-42 kDa. In all the cases, nearly complete sequence specific resonance assignments (> 95%) are obtained. Furthermore, the reliability of the program has been tested by deleting sets of chemical shifts randomly from the master_list created for the test proteins.

PMID: 10921777 [PubMed - indexed for MEDLINE]



Source: PubMed
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Automated analysis of protein NMR assignments and structures.
Automated analysis of protein NMR assignments and structures. Related Articles Automated analysis of protein NMR assignments and structures. Chem Rev. 2004 Aug;104(8):3541-56 Authors: Baran MC, Huang YJ, Moseley HN, Montelione GT
nmrlearner Journal club 0 11-24-2010 10:01 PM
[NMR paper] Smartnotebook: a semi-automated approach to protein sequential NMR resonance assignme
Smartnotebook: a semi-automated approach to protein sequential NMR resonance assignments. Related Articles Smartnotebook: a semi-automated approach to protein sequential NMR resonance assignments. J Biomol NMR. 2003 Dec;27(4):313-21 Authors: Slupsky CM, Boyko RF, Booth VK, Sykes BD Complete and accurate NMR spectral assignment is a prerequisite for high-throughput automated structure determination of biological macromolecules. However, completely automated assignment procedures generally encounter difficulties for all but the most ideal data...
nmrlearner Journal club 0 11-24-2010 09:16 PM
[NMR paper] Automated protein NMR resonance assignments.
Automated protein NMR resonance assignments. Related Articles Automated protein NMR resonance assignments. Proc IEEE Comput Soc Bioinform Conf. 2003;2:197-208 Authors: Wan X, Xu D, Slupsky CM, Lin G NMR resonance peak assignment is one of the key steps in solving an NMR protein structure. The assignment process links resonance peaks to individual residues of the target protein sequence, providing the prerequisite for establishing intra- and inter-residue spatial relationships between atoms. The assignment process is tedious and time-consuming,...
nmrlearner Journal club 0 11-24-2010 09:01 PM
[NMR paper] Automated analysis of NMR assignments and structures for proteins.
Automated analysis of NMR assignments and structures for proteins. Related Articles Automated analysis of NMR assignments and structures for proteins. Curr Opin Struct Biol. 1999 Oct;9(5):635-42 Authors: Moseley HN, Montelione GT Recent developments in protein NMR technology have provided spectral data that are highly amenable to analysis by advanced computer software systems. Specific data collection strategies, coupled with these computer programs, allow automated analysis of extensive backbone and sidechain resonance assignments and...
nmrlearner Journal club 0 11-18-2010 08:31 PM
[NMR paper] An automated approach for defining core atoms and domains in an ensemble of NMR-deriv
An automated approach for defining core atoms and domains in an ensemble of NMR-derived protein structures. Related Articles An automated approach for defining core atoms and domains in an ensemble of NMR-derived protein structures. Protein Eng. 1997 Jun;10(6):737-41 Authors: Kelley LA, Gardner SP, Sutcliffe MJ A single NMR-derived protein structure is usually deposited as an ensemble containing many structures, each consistent with the restraint set used. The number of NMR-derived structures deposited in the Protein Data Bank (PDB) is...
nmrlearner Journal club 0 08-22-2010 03:31 PM
[NMR paper] An automated approach for defining core atoms and domains in an ensemble of NMR-deriv
An automated approach for defining core atoms and domains in an ensemble of NMR-derived protein structures. Related Articles An automated approach for defining core atoms and domains in an ensemble of NMR-derived protein structures. Protein Eng. 1997 Jun;10(6):737-41 Authors: Kelley LA, Gardner SP, Sutcliffe MJ A single NMR-derived protein structure is usually deposited as an ensemble containing many structures, each consistent with the restraint set used. The number of NMR-derived structures deposited in the Protein Data Bank (PDB) is...
nmrlearner Journal club 0 08-22-2010 03:03 PM
[NMR paper] An automated approach for clustering an ensemble of NMR-derived protein structures in
An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies. Related Articles An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies. Protein Eng. 1996 Nov;9(11):1063-5 Authors: Kelley LA, Gardner SP, Sutcliffe MJ
nmrlearner Journal club 0 08-22-2010 02:20 PM
A probabilistic approach for validating protein NMR chemical shift assignments
Abstract It has been estimated that more than 20% of the proteins in the BMRB are improperly referenced and that about 1% of all chemical shift assignments are mis-assigned. These statistics also reflect the likelihood that any newly assigned protein will have shift assignment or shift referencing errors. The relatively high frequency of these errors continues to be a concern for the biomolecular NMR community. While several programs do exist to detect and/or correct chemical shift mis-referencing or chemical shift mis-assignments, most can only do one, or the other. The one program...
nmrlearner Journal club 0 08-14-2010 04:19 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 - 2018, 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 04:27 AM.


Map