Literature DB >> 30125102

Applications of Parametrized NMR Spin Systems of Small Molecules.

Hesam Dashti, Jonathan R Wedell, William M Westler, Marco Tonelli, David Aceti, Gaya K Amarasinghe1, John L Markley, Hamid R Eghbalnia.   

Abstract

We have developed technology for producing accurate spectral fingerprints of small molecules through modeling of NMR spin system matrices to encapsulate their chemical shifts and scalar couplings. We describe here how libraries of these spin systems utilizing unique and reproducible atom numbering can be used to improve NMR-based ligand screening and metabolomics studies. We introduce new Web services that facilitate the analysis of NMR spectra of mixtures of small molecules to yield their identification and quantification. The library of parametrized compounds has been expanded to cover simulations of 1H NMR spectra at a variety of magnetic fields of more than 1100 compounds, included are many common metabolites and a library of drug-like molecular fragments used in ligand screening. The compound library and related Web services are freely available from http://gissmo.nmrfam.wisc.edu/ .

Entities:  

Year:  2018        PMID: 30125102      PMCID: PMC6201686          DOI: 10.1021/acs.analchem.8b02660

Source DB:  PubMed          Journal:  Anal Chem        ISSN: 0003-2700            Impact factor:   6.986


  11 in total

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

Authors:  Marion Pupier; Jean-Marc Nuzillard; Julien Wist; Nils E Schlörer; Stefan Kuhn; Mate Erdelyi; Christoph Steinbeck; Antony J Williams; Craig Butts; Tim D W Claridge; Bozhana Mikhova; Wolfgang Robien; Hesam Dashti; Hamid R Eghbalnia; Christophe Farès; Christian Adam; Pavel Kessler; Fabrice Moriaud; Mikhail Elyashberg; Dimitris Argyropoulos; Manuel Pérez; Patrick Giraudeau; Roberto R Gil; Paul Trevorrow; Damien Jeannerat
Journal:  Magn Reson Chem       Date:  2018-05-16       Impact factor: 2.447

2.  Metabolic Evidence of Diminished Lipid Oxidation in Women With Polycystic Ovary Syndrome.

Authors:  Leah D Whigham; Daniel E Butz; Hesam Dashti; Marco Tonelli; Luann K Johnson; Mark E Cook; Warren P Porter; Hamid R Eghbalnia; John L Markley; Steven R Lindheim; Dale A Schoeller; David H Abbott; Fariba M Assadi-Porter
Journal:  Curr Metabolomics       Date:  2014

3.  NMRbox: A Resource for Biomolecular NMR Computation.

Authors:  Mark W Maciejewski; Adam D Schuyler; Michael R Gryk; Ion I Moraru; Pedro R Romero; Eldon L Ulrich; Hamid R Eghbalnia; Miron Livny; Frank Delaglio; Jeffrey C Hoch
Journal:  Biophys J       Date:  2017-04-25       Impact factor: 4.033

4.  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

5.  HMDB 3.0--The Human Metabolome Database in 2013.

Authors:  David S Wishart; Timothy Jewison; An Chi Guo; Michael Wilson; Craig Knox; Yifeng Liu; Yannick Djoumbou; Rupasri Mandal; Farid Aziat; Edison Dong; Souhaila Bouatra; Igor Sinelnikov; David Arndt; Jianguo Xia; Philip Liu; Faizath Yallou; Trent Bjorndahl; Rolando Perez-Pineiro; Roman Eisner; Felicity Allen; Vanessa Neveu; Russ Greiner; Augustin Scalbert
Journal:  Nucleic Acids Res       Date:  2012-11-17       Impact factor: 16.971

6.  HMDB: the Human Metabolome Database.

Authors:  David S Wishart; Dan Tzur; Craig Knox; Roman Eisner; An Chi Guo; Nelson Young; Dean Cheng; Kevin Jewell; David Arndt; Summit Sawhney; Chris Fung; Lisa Nikolai; Mike Lewis; Marie-Aude Coutouly; Ian Forsythe; Peter Tang; Savita Shrivastava; Kevin Jeroncic; Paul Stothard; Godwin Amegbey; David Block; David D Hau; James Wagner; Jessica Miniaci; Melisa Clements; Mulu Gebremedhin; Natalie Guo; Ying Zhang; Gavin E Duggan; Glen D Macinnis; Alim M Weljie; Reza Dowlatabadi; Fiona Bamforth; Derrick Clive; Russ Greiner; Liang Li; Tom Marrie; Brian D Sykes; Hans J Vogel; Lori Querengesser
Journal:  Nucleic Acids Res       Date:  2007-01       Impact factor: 16.971

7.  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

8.  HMDB 4.0: the human metabolome database for 2018.

Authors:  David S Wishart; Yannick Djoumbou Feunang; Ana Marcu; An Chi Guo; Kevin Liang; Rosa Vázquez-Fresno; Tanvir Sajed; Daniel Johnson; Carin Li; Naama Karu; Zinat Sayeeda; Elvis Lo; Nazanin Assempour; Mark Berjanskii; Sandeep Singhal; David Arndt; Yonjie Liang; Hasan Badran; Jason Grant; Arnau Serra-Cayuela; Yifeng Liu; Rupa Mandal; Vanessa Neveu; Allison Pon; Craig Knox; Michael Wilson; Claudine Manach; Augustin Scalbert
Journal:  Nucleic Acids Res       Date:  2018-01-04       Impact factor: 16.971

9.  BioMagResBank.

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.  NMRFx Processor: a cross-platform NMR data processing program.

Authors:  Michael Norris; Bayard Fetler; Jan Marchant; Bruce A Johnson
Journal:  J Biomol NMR       Date:  2016-07-25       Impact factor: 2.835

View more
  6 in total

1.  BioMagResBank (BMRB) as a Resource for Structural Biology.

Authors:  Pedro R Romero; Naohiro Kobayashi; Jonathan R Wedell; Kumaran Baskaran; Takeshi Iwata; Masashi Yokochi; Dimitri Maziuk; Hongyang Yao; Toshimichi Fujiwara; Genji Kurusu; Eldon L Ulrich; Jeffrey C Hoch; John L Markley
Journal:  Methods Mol Biol       Date:  2020

2.  Fragment screening targeting Ebola virus nucleoprotein C-terminal domain identifies lead candidates.

Authors:  David J Aceti; Hamza Ahmed; William M Westler; Chao Wu; Hesam Dashti; Marco Tonelli; Hamid Eghbalnia; Gaya K Amarasinghe; John L Markley
Journal:  Antiviral Res       Date:  2020-05-21       Impact factor: 5.970

3.  Predicting T-cell quality during manufacturing through an artificial intelligence-based integrative multiomics analytical platform.

Authors:  Valerie Y Odeh-Couvertier; Nathan J Dwarshuis; Maxwell B Colonna; Bruce L Levine; Arthur S Edison; Theresa Kotanchek; Krishnendu Roy; Wandaliz Torres-Garcia
Journal:  Bioeng Transl Med       Date:  2022-01-04

4.  NMR-Based Quantum Mechanical Analysis Builds Trust and Orthogonality in Structural Analysis: The Case of a Bisdesmosidic Triglycoside as Withania somnifera Aerial Parts Marker.

Authors:  Sitaram Bhavaraju; David Taylor; Matthias Niemitz; David C Lankin; Anton Bzhelyansky; Gabriel I Giancaspro; Yang Liu; Guido F Pauli
Journal:  J Nat Prod       Date:  2021-02-24       Impact factor: 4.050

5.  Probabilistic identification of saccharide moieties in biomolecules and their protein complexes.

Authors:  Hesam Dashti; William M Westler; Jonathan R Wedell; Olga V Demler; Hamid R Eghbalnia; John L Markley; Samia Mora
Journal:  Sci Data       Date:  2020-07-03       Impact factor: 6.444

Review 6.  Automatic 1D 1H NMR Metabolite Quantification for Bioreactor Monitoring.

Authors:  Roy Chih Chung Wang; David A Campbell; James R Green; Miroslava Čuperlović-Culf
Journal:  Metabolites       Date:  2021-03-09
  6 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.