Literature DB >> 26724815

Probabilistic validation of protein NMR chemical shift assignments.

Hesam Dashti1,2, Marco Tonelli2, Woonghee Lee2, William M Westler2, Gabriel Cornilescu2, Eldon L Ulrich3, John L Markley4,5.   

Abstract

Data validation plays an important role in ensuring the reliability and reproducibility of studies. NMR investigations of the functional properties, dynamics, chemical kinetics, and structures of proteins depend critically on the correctness of chemical shift assignments. We present a novel probabilistic method named ARECA for validating chemical shift assignments that relies on the nuclear Overhauser effect data . ARECA has been evaluated through its application to 26 case studies and has been shown to be complementary to, and usually more reliable than, approaches based on chemical shift databases. ARECA is available online at http://areca.nmrfam.wisc.edu/.

Entities:  

Keywords:  NMR chemical shift assignments; NOESY experiment; Probabilistic method; Validation

Mesh:

Substances:

Year:  2016        PMID: 26724815      PMCID: PMC4744101          DOI: 10.1007/s10858-015-0007-8

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


  28 in total

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Journal:  J Biomol NMR       Date:  2004-04       Impact factor: 2.835

3.  NMR studies of protein-ligand interactions.

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Journal:  Methods Mol Biol       Date:  2012

4.  A probabilistic approach for validating protein NMR chemical shift assignments.

Authors:  Bowei Wang; Yunjun Wang; David S Wishart
Journal:  J Biomol NMR       Date:  2010-05-06       Impact factor: 2.835

5.  An NMR method to study protein-protein interactions.

Authors:  Noritaka Nishida; Ichio Shimada
Journal:  Methods Mol Biol       Date:  2012

6.  Increased reliability of nuclear magnetic resonance protein structures by consensus structure bundles.

Authors:  Lena Buchner; Peter Güntert
Journal:  Structure       Date:  2015-01-08       Impact factor: 5.006

7.  Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications.

Authors:  Liya Wang; Hamid R Eghbalnia; Arash Bahrami; John L Markley
Journal:  J Biomol NMR       Date:  2005-05       Impact factor: 2.835

8.  Nuclear magnetic resonance spectroscopy. Ring-current effects on carbon-13 chemical shifts.

Authors:  R D Vernet; V Boekelheide
Journal:  Proc Natl Acad Sci U S A       Date:  1974-08       Impact factor: 11.205

9.  The J-UNIO protocol for automated protein structure determination by NMR in solution.

Authors:  Pedro Serrano; Bill Pedrini; Biswaranjan Mohanty; Michael Geralt; Torsten Herrmann; Kurt Wüthrich
Journal:  J Biomol NMR       Date:  2012-07-03       Impact factor: 2.835

10.  Validation of archived chemical shifts through atomic coordinates.

Authors:  Wolfgang Rieping; Wim F Vranken
Journal:  Proteins       Date:  2010-08-15
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  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.  NMR assignments of sparsely labeled proteins using a genetic algorithm.

Authors:  Qi Gao; Gordon R Chalmers; Kelley W Moremen; James H Prestegard
Journal:  J Biomol NMR       Date:  2017-03-13       Impact factor: 2.835

3.  PINE-SPARKY.2 for automated NMR-based protein structure research.

Authors:  Woonghee Lee; John L Markley
Journal:  Bioinformatics       Date:  2018-05-01       Impact factor: 6.937

4.  Solution structure of human myeloid-derived growth factor suggests a conserved function in the endoplasmic reticulum.

Authors:  Valeriu Bortnov; Marco Tonelli; Woonghee Lee; Ziqing Lin; Douglas S Annis; Omar N Demerdash; Alex Bateman; Julie C Mitchell; Ying Ge; John L Markley; Deane F Mosher
Journal:  Nat Commun       Date:  2019-12-09       Impact factor: 14.919

5.  POKY software tools encapsulating assignment strategies for solution and solid-state protein NMR data.

Authors:  Ira Manthey; Marco Tonelli; Lawrence Clos Ii; Mehdi Rahimi; John L Markley; Woonghee Lee
Journal:  J Struct Biol X       Date:  2022-08-28

6.  Integrative NMR for biomolecular research.

Authors:  Woonghee Lee; Gabriel Cornilescu; Hesam Dashti; Hamid R Eghbalnia; Marco Tonelli; William M Westler; Samuel E Butcher; Katherine A Henzler-Wildman; John L Markley
Journal:  J Biomol NMR       Date:  2016-03-29       Impact factor: 2.835

  6 in total

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