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 11-24-2010, 09:01 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 20,161
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 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, which could take many weeks. Though there exist a number of computer programs to assist the assignment process, many NMR labs are still doing the assignments manually to ensure quality. This paper presents (1) a new scoring system for mapping spin systems to residues, (2) an automated adjacency information extraction procedure from NMR spectra, and (3) a very fast assignment algorithm based on our previous proposed greedy filtering method and a maximum matching algorithm to automate the assignment process. The computational tests on 70 instances of (pseudo) experimental NMR data of 14 proteins demonstrate that the new score scheme has much better discerning power with the aid of adjacency information between spin systems simulated across various NMR spectra. Typically, with automated extraction of adjacency information, our method achieves nearly complete assignments for most of the proteins. The experiment shows very promising perspective that the fast automated assignment algorithm together with the new score scheme and automated adjacency extraction may be ready for practical use.

PMID: 16452794 [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] 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...
nmrlearner Journal club 0 11-18-2010 09:15 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
Automated protein resonance assignments of magic angle spinning solid-state NMR spect
Automated protein resonance assignments of magic angle spinning solid-state NMR spectra of β1 immunoglobulin binding domain of protein G (GB1) Abstract Magic-angle spinning solid-state NMR (MAS SSNMR) represents a fast developing experimental technique with great potential to provide structural and dynamics information for proteins not amenable to other methods. However, few automated analysis tools are currently available for MAS SSNMR. We present a methodology for automating protein resonance assignments of MAS SSNMR spectral data and its application to experimental peak lists of the...
nmrlearner Journal club 0 10-15-2010 05:16 PM
Automated protein resonance assignments of magic angle spinning solid-state NMR spect
Automated protein resonance assignments of magic angle spinning solid-state NMR spectra of ?1 immunoglobulin binding domain of protein G (GB1). Related Articles Automated protein resonance assignments of magic angle spinning solid-state NMR spectra of ?1 immunoglobulin binding domain of protein G (GB1). J Biomol NMR. 2010 Oct 8; Authors: Moseley HN, Sperling LJ, Rienstra CM Magic-angle spinning solid-state NMR (MAS SSNMR) represents a fast developing experimental technique with great potential to provide structural and dynamics information for...
nmrlearner Journal club 0 10-12-2010 02:52 PM
[NMR paper] Automated analysis of protein NMR assignments using methods from artificial intellige
Automated analysis of protein NMR assignments using methods from artificial intelligence. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Automated analysis of protein NMR assignments using methods from artificial intelligence. J Mol Biol. 1997 Jun 20;269(4):592-610 Authors: Zimmerman DE, Kulikowski CA, Huang Y, Feng W, Tashiro M, Shimotakahara S, Chien C, Powers R, Montelione GT An expert system for determining resonance assignments from NMR spectra of proteins is...
nmrlearner Journal club 0 08-22-2010 03:31 PM
[NMR paper] Automated analysis of protein NMR assignments using methods from artificial intellige
Automated analysis of protein NMR assignments using methods from artificial intelligence. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Automated analysis of protein NMR assignments using methods from artificial intelligence. J Mol Biol. 1997 Jun 20;269(4):592-610 Authors: Zimmerman DE, Kulikowski CA, Huang Y, Feng W, Tashiro M, Shimotakahara S, Chien C, Powers R, Montelione GT An expert system for determining resonance assignments from NMR spectra of proteins is...
nmrlearner Journal club 0 08-22-2010 03:03 PM


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 - 2020, 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 10:36 AM.


Map