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 08-21-2010, 11:53 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,135
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 constraint reasoning system for automating sequence-specific resonance assignments

A constraint reasoning system for automating sequence-specific resonance assignments from multidimensional protein NMR spectra.

Related Articles A constraint reasoning system for automating sequence-specific resonance assignments from multidimensional protein NMR spectra.

Proc Int Conf Intell Syst Mol Biol. 1993;1:447-55

Authors: Zimmerman DE, Kulikowski CA, Montelione GT

AUTOASSIGN is a prototype expert system designed to aid in the determination of protein structure from nuclear magnetic resonance (NMR) measurements. In this paper we focus on one of the key steps of this process, the assignment of the observed NMR signals to specific atomic nuclei in the protein; i.e. the determination of sequence-specific resonance assignments. Recently developed triple-resonance (1H, 15N, and 13C) NMR experiments [Montelione et al., 1992] have provided an important breakthrough in this field, as the resulting data are more amenable to automated analysis than data sets generated using conventional strategies [Wuethrich, 1986]. The "assignment problem" can be stated as a constraint satisfaction problem (CSP) with some added complexities. There is very little internal structure to the problem, making it difficult to apply subgoaling and problem decomposition. Moreover, the data used to generate the constraints are incomplete, non-unique, and noisy, and constraints emerge dynamically as analysis progresses. The traditional inference engine is replaced by a set of very tightly-coupled modules which enforce extensive constraint propagation, with state information distributed over the objects whose relationships are being constrained. AUTOASSIGN provides correct and nearly complete resonance assignments with both simulated and real 3D triple-resonance data for a 72 amino acid protein.

PMID: 7584369 [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] Sequence-specific NMR resonance assignments of the backbone atoms for the olfactory m
Sequence-specific NMR resonance assignments of the backbone atoms for the olfactory marker protein, OMP. Related Articles Sequence-specific NMR resonance assignments of the backbone atoms for the olfactory marker protein, OMP. J Biomol NMR. 2000 Aug;17(4):353-4 Authors: Baldisseri DM, Margolis JW, Omotosho PA, Volkman BF, Margolis FL
nmrlearner Journal club 0 11-19-2010 08:29 PM
[NMR paper] Sequence-specific 1H NMR resonance assignments and secondary structure of human apoli
Sequence-specific 1H NMR resonance assignments and secondary structure of human apolipoprotein C-I in the presence of sodium dodecyl sulfate. Related Articles Sequence-specific 1H NMR resonance assignments and secondary structure of human apolipoprotein C-I in the presence of sodium dodecyl sulfate. Biochem Cell Biol. 1998;76(2-3):267-75 Authors: Rozek A, Sparrow JT, Weisgraber KH, Cushley RJ Apolipoprotein (apo) C-I is a 57-residue exchangeable plasma protein distributed mainly in high and very low density lipoprotein. In this report we...
nmrlearner Journal club 0 11-17-2010 11:06 PM
[NMR paper] Sequence-specific resonance assignments of the 1H-NMR spectra and structural characte
Sequence-specific resonance assignments of the 1H-NMR spectra and structural characterization in solution of the HIV-1 transframe protein p6. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles Sequence-specific resonance assignments of the 1H-NMR spectra and structural characterization in solution of the HIV-1 transframe protein p6. Eur J Biochem. 1996 Apr 15;237(2):383-92 Authors: Beissinger M, Paulus C, Bayer P, Wolf H, Rösch P, Wagner R ...
nmrlearner Journal club 0 08-22-2010 02:27 PM
[NMR paper] Composition and sequence specific resonance assignments of the heterogeneous N-linked
Composition and sequence specific resonance assignments of the heterogeneous N-linked glycan in the 13.6 kDa adhesion domain of human CD2 as determined by NMR on the intact glycoprotein. Related Articles Composition and sequence specific resonance assignments of the heterogeneous N-linked glycan in the 13.6 kDa adhesion domain of human CD2 as determined by NMR on the intact glycoprotein. Biochemistry. 1995 Feb 7;34(5):1622-34 Authors: Wyss DF, Choi JS, Wagner G CD2, a T cell specific surface adhesion receptor, is critically important for T...
nmrlearner Journal club 0 08-22-2010 03:41 AM
[NMR paper] Sequence-specific resonance assignments of the 1H-NMR spectra of a synthetic, biologi
Sequence-specific resonance assignments of the 1H-NMR spectra of a synthetic, biologically active EIAV Tat protein. Related Articles Sequence-specific resonance assignments of the 1H-NMR spectra of a synthetic, biologically active EIAV Tat protein. Biochemistry. 1993 Aug 24;32(33):8439-45 Authors: Willbold D, Krüger U, Frank R, Rosin-Arbesfeld R, Gazit A, Yaniv A, Rösch P The equine infectious anemia virus (EIAV) trans-activating (Tat) protein is a close homologue of the human immunodeficiency virus (HIV) Tat protein. Both of these proteins...
nmrlearner Journal club 0 08-22-2010 03:01 AM
[NMR paper] Sequence-specific 1H NMR resonance assignments of Bacillus subtilis HPr: use of spect
Sequence-specific 1H NMR resonance assignments of Bacillus subtilis HPr: use of spectra obtained from mutants to resolve spectral overlap. Related Articles Sequence-specific 1H NMR resonance assignments of Bacillus subtilis HPr: use of spectra obtained from mutants to resolve spectral overlap. Biochemistry. 1990 Aug 7;29(31):7191-200 Authors: Wittekind M, Reizer J, Klevit RE On the basis of an analysis of two-dimensional 1H NMR spectra, the complete sequence-specific 1H NMR assignments are presented for the phosphocarrier protein HPr from the...
nmrlearner Journal club 0 08-21-2010 11:04 PM
[NMR paper] An efficient NMR approach for obtaining sequence-specific resonance assignments of la
An efficient NMR approach for obtaining sequence-specific resonance assignments of larger proteins based on multiple isotopic labeling. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles An efficient NMR approach for obtaining sequence-specific resonance assignments of larger proteins based on multiple isotopic labeling. FEBS Lett. 1990 Jun 18;266(1-2):155-8 Authors: Ikura M, Krinks M, Torchia DA, Bax A By simultaneously incorporating in a protein 13C-carbonyl- and...
nmrlearner Journal club 0 08-21-2010 10:48 PM
[NMR paper] Sequence-specific [1H]NMR resonance assignments and secondary structure identificatio
Sequence-specific NMR resonance assignments and secondary structure identification for 1- and 2-zinc finger constructs from SW15. A hydrophobic core involving four invariant residues. Related Articles Sequence-specific NMR resonance assignments and secondary structure identification for 1- and 2-zinc finger constructs from SW15. A hydrophobic core involving four invariant residues. FEBS Lett. 1990 Mar 26;262(2):179-84 Authors: Neuhaus D, Nakaseko Y, Nagai K, Klug A Complete NMR resonance assignments are presented for the second of the three...
nmrlearner Journal club 0 08-21-2010 10:48 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 - 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 10:49 PM.


Map