Literature DB >> 29656574

NMReDATA, a standard to report the NMR assignment and parameters of organic compounds.

Marion Pupier1, Jean-Marc Nuzillard2, Julien Wist3, Nils E Schlörer4, Stefan Kuhn4, Mate Erdelyi5, Christoph Steinbeck6, Antony J Williams7, Craig Butts8, Tim D W Claridge9, Bozhana Mikhova10, Wolfgang Robien11, Hesam Dashti12, Hamid R Eghbalnia12, Christophe Farès13, Christian Adam14, Pavel Kessler15, Fabrice Moriaud16, Mikhail Elyashberg17, Dimitris Argyropoulos18, Manuel Pérez19, Patrick Giraudeau20,21, Roberto R Gil22, Paul Trevorrow23, Damien Jeannerat1.   

Abstract

Even though NMR has found countless applications in the field of small molecule characterization, there is no standard file format available for the NMR data relevant to structure characterization of small molecules. A new format is therefore introduced to associate the NMR parameters extracted from 1D and 2D spectra of organic compounds to the proposed chemical structure. These NMR parameters, which we shall call NMReDATA (for nuclear magnetic resonance extracted data), include chemical shift values, signal integrals, intensities, multiplicities, scalar coupling constants, lists of 2D correlations, relaxation times, and diffusion rates. The file format is an extension of the existing Structure Data Format, which is compatible with the commonly used MOL format. The association of an NMReDATA file with the raw and spectral data from which it originates constitutes an NMR record. This format is easily readable by humans and computers and provides a simple and efficient way for disseminating results of structural chemistry investigations, allowing automatic verification of published results, and for assisting the constitution of highly needed open-source structural databases.
Copyright © 2018 John Wiley & Sons, Ltd.

Entities:  

Keywords:  Automatic structure verification; NMR; NMR record; NMReDATA; computer-assisted structure elucidation (CASE); data format; database; extracted data

Mesh:

Substances:

Year:  2018        PMID: 29656574      PMCID: PMC6226248          DOI: 10.1002/mrc.4737

Source DB:  PubMed          Journal:  Magn Reson Chem        ISSN: 0749-1581            Impact factor:   2.447


  23 in total

Review 1.  Structural revisions of natural products by Computer-Assisted Structure Elucidation (CASE) systems.

Authors:  Mikhail Elyashberg; Antony J Williams; Kirill Blinov
Journal:  Nat Prod Rep       Date:  2010-05-18       Impact factor: 13.423

2.  Assigning stereochemistry to single diastereoisomers by GIAO NMR calculation: the DP4 probability.

Authors:  Steven G Smith; Jonathan M Goodman
Journal:  J Am Chem Soc       Date:  2010-09-22       Impact factor: 15.419

3.  Facilitating quality control for spectra assignments of small organic molecules: nmrshiftdb2--a free in-house NMR database with integrated LIMS for academic service laboratories.

Authors:  Stefan Kuhn; Nils E Schlörer
Journal:  Magn Reson Chem       Date:  2015-05-21       Impact factor: 2.447

4.  MRC's proposal to change the submission procedure for the future submission of assignment papers.

Authors: 
Journal:  Magn Reson Chem       Date:  2017-08-30       Impact factor: 2.447

5.  nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data.

Authors:  Daniel Schober; Daniel Jacob; Michael Wilson; Joseph A Cruz; Ana Marcu; Jason R Grant; Annick Moing; Catherine Deborde; Luis F de Figueiredo; Kenneth Haug; Philippe Rocca-Serra; John Easton; Timothy M D Ebbels; Jie Hao; Christian Ludwig; Ulrich L Günther; Antonio Rosato; Matthias S Klein; Ian A Lewis; Claudio Luchinat; Andrew R Jones; Arturas Grauslys; Martin Larralde; Masashi Yokochi; Naohiro Kobayashi; Andrea Porzel; Julian L Griffin; Mark R Viant; David S Wishart; Christoph Steinbeck; Reza M Salek; Steffen Neumann
Journal:  Anal Chem       Date:  2017-12-14       Impact factor: 6.986

Review 6.  Human- and computer-accessible 2D correlation data for a more reliable structure determination of organic compounds. Future roles of researchers, software developers, spectrometer managers, journal editors, reviewers, publisher and database managers toward artificial-intelligence analysis of NMR spectra.

Authors:  Damien Jeannerat
Journal:  Magn Reson Chem       Date:  2016-10-02       Impact factor: 2.447

7.  Spin System Modeling of Nuclear Magnetic Resonance Spectra for Applications in Metabolomics and Small Molecule Screening.

Authors:  Hesam Dashti; William M Westler; Marco Tonelli; Jonathan R Wedell; John L Markley; Hamid R Eghbalnia
Journal:  Anal Chem       Date:  2017-11-07       Impact factor: 6.986

8.  Unique identifiers for small molecules enable rigorous labeling of their atoms.

Authors:  Hesam Dashti; William M Westler; John L Markley; Hamid R Eghbalnia
Journal:  Sci Data       Date:  2017-05-23       Impact factor: 6.444

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Authors:  Eldon L Ulrich; Hideo Akutsu; Jurgen F Doreleijers; Yoko Harano; Yannis E Ioannidis; Jundong Lin; Miron Livny; Steve Mading; Dimitri Maziuk; Zachary Miller; Eiichi Nakatani; Christopher F Schulte; David E Tolmie; R Kent Wenger; Hongyang Yao; John L Markley
Journal:  Nucleic Acids Res       Date:  2007-11-04       Impact factor: 16.971

10.  Essential parameters for structural analysis and dereplication by (1)H NMR spectroscopy.

Authors:  Guido F Pauli; Shao-Nong Chen; David C Lankin; Jonathan Bisson; Ryan J Case; Lucas R Chadwick; Tanja Gödecke; Taichi Inui; Aleksej Krunic; Birgit U Jaki; James B McAlpine; Shunyan Mo; José G Napolitano; Jimmy Orjala; Juuso Lehtivarjo; Samuli-Petrus Korhonen; Matthias Niemitz
Journal:  J Nat Prod       Date:  2014-06-04       Impact factor: 4.050

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  15 in total

1.  Applications of Parametrized NMR Spin Systems of Small Molecules.

Authors:  Hesam Dashti; Jonathan R Wedell; William M Westler; Marco Tonelli; David Aceti; Gaya K Amarasinghe; John L Markley; Hamid R Eghbalnia
Journal:  Anal Chem       Date:  2018-08-24       Impact factor: 6.986

2.  Oxygenated Cyclohexene Derivatives and Other Constituents from the Roots of Monanthotaxis trichocarpa.

Authors:  Gasper Maeda; Jelle van der Wal; Arvind Kumar Gupta; Joan J E Munissi; Andreas Orthaber; Per Sunnerhagen; Stephen S Nyandoro; Máté Erdélyi
Journal:  J Nat Prod       Date:  2020-01-27       Impact factor: 4.050

3.  Crystal Structures and Cytotoxicity of ent-Kaurane-Type Diterpenoids from Two Aspilia Species.

Authors:  Souaibou Yaouba; Arto Valkonen; Paolo Coghi; Jiaying Gao; Eric M Guantai; Solomon Derese; Vincent K W Wong; Máté Erdélyi; Abiy Yenesew
Journal:  Molecules       Date:  2018-12-04       Impact factor: 4.411

4.  Automated evaluation of consistency within the PubChem Compound database.

Authors:  Hesam Dashti; Jonathan R Wedell; William M Westler; John L Markley; Hamid R Eghbalnia
Journal:  Sci Data       Date:  2019-02-19       Impact factor: 6.444

5.  Workflows Allowing Creation of Journal Article Supporting Information and Findable, Accessible, Interoperable, and Reusable (FAIR)-Enabled Publication of Spectroscopic Data.

Authors:  Agustin Barba; Santiago Dominguez; Carlos Cobas; David P Martinsen; Charles Romain; Henry S Rzepa; Felipe Seoane
Journal:  ACS Omega       Date:  2019-02-14

6.  Signal Deconvolution and Noise Factor Analysis Based on a Combination of Time-Frequency Analysis and Probabilistic Sparse Matrix Factorization.

Authors:  Shunji Yamada; Atsushi Kurotani; Eisuke Chikayama; Jun Kikuchi
Journal:  Int J Mol Sci       Date:  2020-04-23       Impact factor: 5.923

7.  Conformational Investigations in Flexible Molecules Using Orientational NMR Constraints in Combination with 3J-Couplings and NOE Distances.

Authors:  Christophe Farès; Julia B Lingnau; Cornelia Wirtz; Ulrich Sternberg
Journal:  Molecules       Date:  2019-12-03       Impact factor: 4.411

8.  Biflavanones, Chalconoids, and Flavonoid Analogues from the Stem Bark of Ochna holstii.

Authors:  Thobias M Kalenga; Monica M Ndoile; Yoseph Atilaw; Pieter J Gilissen; Joan J E Munissi; Anastasia Rudenko; Catarina Bourgard; Per Sunnerhagen; Stephen S Nyandoro; Mate Erdelyi
Journal:  J Nat Prod       Date:  2021-01-29       Impact factor: 4.050

Review 9.  The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research.

Authors:  James B McAlpine; Shao-Nong Chen; Andrei Kutateladze; John B MacMillan; Giovanni Appendino; Andersson Barison; Mehdi A Beniddir; Maique W Biavatti; Stefan Bluml; Asmaa Boufridi; Mark S Butler; Robert J Capon; Young H Choi; David Coppage; Phillip Crews; Michael T Crimmins; Marie Csete; Pradeep Dewapriya; Joseph M Egan; Mary J Garson; Grégory Genta-Jouve; William H Gerwick; Harald Gross; Mary Kay Harper; Precilia Hermanto; James M Hook; Luke Hunter; Damien Jeannerat; Nai-Yun Ji; Tyler A Johnson; David G I Kingston; Hiroyuki Koshino; Hsiau-Wei Lee; Guy Lewin; Jie Li; Roger G Linington; Miaomiao Liu; Kerry L McPhail; Tadeusz F Molinski; Bradley S Moore; Joo-Won Nam; Ram P Neupane; Matthias Niemitz; Jean-Marc Nuzillard; Nicholas H Oberlies; Fernanda M M Ocampos; Guohui Pan; Ronald J Quinn; D Sai Reddy; Jean-Hugues Renault; José Rivera-Chávez; Wolfgang Robien; Carla M Saunders; Thomas J Schmidt; Christoph Seger; Ben Shen; Christoph Steinbeck; Hermann Stuppner; Sonja Sturm; Orazio Taglialatela-Scafati; Dean J Tantillo; Robert Verpoorte; Bin-Gui Wang; Craig M Williams; Philip G Williams; Julien Wist; Jian-Min Yue; Chen Zhang; Zhengren Xu; Charlotte Simmler; David C Lankin; Jonathan Bisson; Guido F Pauli
Journal:  Nat Prod Rep       Date:  2018-07-13       Impact factor: 13.423

10.  An automated framework for NMR chemical shift calculations of small organic molecules.

Authors:  Yasemin Yesiltepe; Jamie R Nuñez; Sean M Colby; Dennis G Thomas; Mark I Borkum; Patrick N Reardon; Nancy M Washton; Thomas O Metz; Justin G Teeguarden; Niranjan Govind; Ryan S Renslow
Journal:  J Cheminform       Date:  2018-10-26       Impact factor: 5.514

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