Literature DB >> 21411039

Advances in automated NMR protein structure determination.

Paul Guerry1, Torsten Herrmann.   

Abstract

Around half of all protein structures solved nowadays using solution-state nuclear magnetic resonance (NMR) spectroscopy have been because of automated data analysis. The pervasiveness of computational approaches in general hides, however, a more nuanced view in which the full variety and richness of the field appears. This review is structured around a comparison of methods associated with three NMR observables: classical nuclear Overhauser effect (NOE) constraint gathering in contrast with more recent chemical shift and residual dipole coupling (RDC) based protocols. In each case, the emphasis is placed on the latest research, covering mainly the past 5 years. By describing both general concepts and representative programs, the objective is to map out a field in which--through the very profusion of approaches--it is all too easy to lose one's bearings.

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Year:  2011        PMID: 21411039     DOI: 10.1017/S0033583510000326

Source DB:  PubMed          Journal:  Q Rev Biophys        ISSN: 0033-5835            Impact factor:   5.318


  32 in total

1.  Reliability of exclusively NOESY-based automated resonance assignment and structure determination of proteins.

Authors:  Elena Schmidt; Peter Güntert
Journal:  J Biomol NMR       Date:  2013-09-15       Impact factor: 2.835

2.  CASD-NMR 2: robust and accurate unsupervised analysis of raw NOESY spectra and protein structure determination with UNIO.

Authors:  Paul Guerry; Viet Dung Duong; Torsten Herrmann
Journal:  J Biomol NMR       Date:  2015-04-28       Impact factor: 2.835

3.  NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary.

Authors:  Emel Maden Yilmaz; Peter Güntert
Journal:  J Biomol NMR       Date:  2015-06-30       Impact factor: 2.835

4.  Systematic evaluation of combined automated NOE assignment and structure calculation with CYANA.

Authors:  Lena Buchner; Peter Güntert
Journal:  J Biomol NMR       Date:  2015-03-22       Impact factor: 2.835

5.  Combined automated NOE assignment and structure calculation with CYANA.

Authors:  Peter Güntert; Lena Buchner
Journal:  J Biomol NMR       Date:  2015-03-24       Impact factor: 2.835

6.  Rapid prediction of multi-dimensional NMR data sets.

Authors:  Sabine Gradmann; Christian Ader; Ines Heinrich; Deepak Nand; Marc Dittmann; Abhishek Cukkemane; Marc van Dijk; Alexandre M J J Bonvin; Martin Engelhard; Marc Baldus
Journal:  J Biomol NMR       Date:  2012-11-10       Impact factor: 2.835

7.  Peakmatch: a simple and robust method for peak list matching.

Authors:  Lena Buchner; Elena Schmidt; Peter Güntert
Journal:  J Biomol NMR       Date:  2013-01-18       Impact factor: 2.835

8.  Automated solid-state NMR resonance assignment of protein microcrystals and amyloids.

Authors:  Elena Schmidt; Julia Gath; Birgit Habenstein; Francesco Ravotti; Kathrin Székely; Matthias Huber; Lena Buchner; Anja Böckmann; Beat H Meier; Peter Güntert
Journal:  J Biomol NMR       Date:  2013-05-21       Impact factor: 2.835

9.  Site-specific NMR mapping and time-resolved monitoring of serine and threonine phosphorylation in reconstituted kinase reactions and mammalian cell extracts.

Authors:  Francois-Xavier Theillet; Honor May Rose; Stamatios Liokatis; Andres Binolfi; Rossukon Thongwichian; Marchel Stuiver; Philipp Selenko
Journal:  Nat Protoc       Date:  2013-06-27       Impact factor: 13.491

10.  CONNJUR R: an annotation strategy for fostering reproducibility in bio-NMR-protein spectral assignment.

Authors:  Matthew Fenwick; Jeffrey C Hoch; Eldon Ulrich; Michael R Gryk
Journal:  J Biomol NMR       Date:  2015-08-08       Impact factor: 2.835

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