Literature DB >> 17031528

A nomenclature and data model to describe NMR experiments.

Rasmus H Fogh1, Wim F Vranken, Wayne Boucher, Tim J Stevens, Ernest D Laue.   

Abstract

Despite ongoing efforts in organising NMR information, there is no consistent and well-described generic standard for naming NMR experiments. The main reason for the absence of a universal naming system is that the information content of the coherence pathways is difficult to describe in full detail. We propose a system that describes the common and generic elements of the coherence pathways produced by pulse sequences. The system itself is formalised by an 'NMR experiment protocol' model, which is described in the Universal Modelling Language (UML) as part of the CCPN data model. Furthermore, normalized experiment names can be derived from this proposed model. We hope this article will stimulate discussion to organise the wealth of NMR experiments, and that by bringing this discussion into the public domain we can improve and expand our proposed system to include as much information and as many NMR experiments as possible.

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Year:  2006        PMID: 17031528     DOI: 10.1007/s10858-006-9076-z

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN: 0925-2738            Impact factor:   2.835


  23 in total

1.  SPINS: standardized protein NMR storage. A data dictionary and object-oriented relational database for archiving protein NMR spectra.

Authors:  Michael C Baran; Hunter N B Moseley; Gurmukh Sahota; Gaetano T Montelione
Journal:  J Biomol NMR       Date:  2002-10       Impact factor: 2.835

2.  Recommendations for the presentation of NMR structures of proteins and nucleic acids.

Authors:  J L Markley; A Bax; Y Arata; C W Hilbers; R Kaptein; B D Sykes; P E Wright; K Wüthrich
Journal:  J Mol Biol       Date:  1998-07-31       Impact factor: 5.469

3.  Three-dimensional NMR spectroscopy of a protein in solution.

Authors:  H Oschkinat; C Griesinger; P J Kraulis; O W Sørensen; R R Ernst; A M Gronenborn; G M Clore
Journal:  Nature       Date:  1988-03-24       Impact factor: 49.962

4.  Overcoming the overlap problem in the assignment of 1H NMR spectra of larger proteins by use of three-dimensional heteronuclear 1H-15N Hartmann-Hahn-multiple quantum coherence and nuclear Overhauser-multiple quantum coherence spectroscopy: application to interleukin 1 beta.

Authors:  D Marion; P C Driscoll; L E Kay; P T Wingfield; A Bax; A M Gronenborn; G M Clore
Journal:  Biochemistry       Date:  1989-07-25       Impact factor: 3.162

5.  Improved three-dimensional 1H-13C-1H correlation spectroscopy of a 13C-labeled protein using constant-time evolution.

Authors:  M Ikura; L E Kay; A Bax
Journal:  J Biomol NMR       Date:  1991-09       Impact factor: 2.835

6.  A 4D HCCH-TOCSY experiment for assigning the side chain 1H and 13C resonances of proteins.

Authors:  E T Olejniczak; R X Xu; S W Fesik
Journal:  J Biomol NMR       Date:  1992-11       Impact factor: 2.835

7.  Two- and three-dimensional HCN experiments for correlating base and sugar resonances in 15N,13C-labeled RNA oligonucleotides.

Authors:  V Sklenár; R D Peterson; M R Rejante; J Feigon
Journal:  J Biomol NMR       Date:  1993-11       Impact factor: 2.835

8.  Amino acid type determination in the sequential assignment procedure of uniformly 13C/15N-enriched proteins.

Authors:  S Grzesiek; A Bax
Journal:  J Biomol NMR       Date:  1993-03       Impact factor: 2.835

9.  A general method for assigning NMR spectra of denatured proteins using 3D HC(CO)NH-TOCSY triple resonance experiments.

Authors:  T M Logan; E T Olejniczak; R X Xu; S W Fesik
Journal:  J Biomol NMR       Date:  1993-03       Impact factor: 2.835

10.  A novel approach for sequential assignment of 1H, 13C, and 15N spectra of proteins: heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin.

Authors:  M Ikura; L E Kay; A Bax
Journal:  Biochemistry       Date:  1990-05-15       Impact factor: 3.162

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  13 in total

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Authors:  Michael R Gryk; Jay Vyas; Mark W Maciejewski
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2010-05       Impact factor: 9.795

Review 2.  Analysis of bacterial biofilms using NMR-based metabolomics.

Authors:  Bo Zhang; Robert Powers
Journal:  Future Med Chem       Date:  2012-06       Impact factor: 3.808

3.  An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database.

Authors:  Naohiro Kobayashi; Yoko Harano; Naoya Tochio; Eiichi Nakatani; Takanori Kigawa; Shigeyuki Yokoyama; Steve Mading; Eldon L Ulrich; John L Markley; Hideo Akutsu; Toshimichi Fujiwara
Journal:  J Biomol NMR       Date:  2012-06-13       Impact factor: 2.835

Review 4.  Bioinformatics and molecular modeling in glycobiology.

Authors:  Martin Frank; Siegfried Schloissnig
Journal:  Cell Mol Life Sci       Date:  2010-04-04       Impact factor: 9.261

5.  Observation of a low-temperature, dynamically driven structural transition in a polypeptide by solid-state NMR spectroscopy.

Authors:  Vikram S Bajaj; Patrick C A van der Wel; Robert G Griffin
Journal:  J Am Chem Soc       Date:  2009-01-14       Impact factor: 15.419

6.  Solution structure and peptide binding of the PTB domain from the AIDA1 postsynaptic signaling scaffolding protein.

Authors:  Ekaterina Smirnova; Riya Shanbhag; Arwa Kurabi; Mehdi Mobli; Jamie J Kwan; Logan W Donaldson
Journal:  PLoS One       Date:  2013-06-14       Impact factor: 3.240

7.  The Protein Data Bank in Europe (PDBe): bringing structure to biology.

Authors:  Sameer Velankar; Gerard J Kleywegt
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2011-03-18

8.  A software framework for analysing solid-state MAS NMR data.

Authors:  Tim J Stevens; Rasmus H Fogh; Wayne Boucher; Victoria A Higman; Frank Eisenmenger; Benjamin Bardiaux; Barth-Jan van Rossum; Hartmut Oschkinat; Ernest D Laue
Journal:  J Biomol NMR       Date:  2011-09-28       Impact factor: 2.835

9.  The use of glycoinformatics in glycochemistry.

Authors:  Thomas Lütteke
Journal:  Beilstein J Org Chem       Date:  2012-06-21       Impact factor: 2.883

10.  PDBe: Protein Data Bank in Europe.

Authors:  S Velankar; C Best; B Beuth; C H Boutselakis; N Cobley; A W Sousa Da Silva; D Dimitropoulos; A Golovin; M Hirshberg; M John; E B Krissinel; R Newman; T Oldfield; A Pajon; C J Penkett; J Pineda-Castillo; G Sahni; S Sen; R Slowley; A Suarez-Uruena; J Swaminathan; G van Ginkel; W F Vranken; K Henrick; G J Kleywegt
Journal:  Nucleic Acids Res       Date:  2009-10-25       Impact factor: 16.971

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