Literature DB >> 18807026

Automated structure determination from NMR spectra.

Peter Güntert1.   

Abstract

Automated methods for protein structure determination by NMR have increasingly gained acceptance and are now widely used for the automated assignment of distance restraints and the calculation of three-dimensional structures. This review gives an overview of the techniques for automated protein structure analysis by NMR, including both NOE-based approaches and methods relying on other experimental data such as residual dipolar couplings and chemical shifts, and presents the FLYA algorithm for the fully automated NMR structure determination of proteins that is suitable to substitute all manual spectra analysis and thus overcomes a major efficiency limitation of the NMR method for protein structure determination.

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Year:  2008        PMID: 18807026     DOI: 10.1007/s00249-008-0367-z

Source DB:  PubMed          Journal:  Eur Biophys J        ISSN: 0175-7571            Impact factor:   1.733


  106 in total

Review 1.  The direct determination of protein structure by NMR without assignment.

Authors:  R Andrew Atkinson; Vladimír Saudek
Journal:  FEBS Lett       Date:  2002-01-02       Impact factor: 4.124

2.  Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.

Authors:  Torsten Herrmann; Peter Güntert; Kurt Wüthrich
Journal:  J Mol Biol       Date:  2002-05-24       Impact factor: 5.469

3.  Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE).

Authors:  Wolfram Gronwald; Sherif Moussa; Ralph Elsner; Astrid Jung; Bernhard Ganslmeier; Jochen Trenner; Werner Kremer; Klaus-Peter Neidig; Hans Robert Kalbitzer
Journal:  J Biomol NMR       Date:  2002-08       Impact factor: 2.835

4.  Toward high-resolution de novo structure prediction for small proteins.

Authors:  Philip Bradley; Kira M S Misura; David Baker
Journal:  Science       Date:  2005-09-16       Impact factor: 47.728

5.  Protein structure determination from NMR chemical shifts.

Authors:  Andrea Cavalli; Xavier Salvatella; Christopher M Dobson; Michele Vendruscolo
Journal:  Proc Natl Acad Sci U S A       Date:  2007-05-29       Impact factor: 11.205

6.  Automated structure determination of proteins with the SAIL-FLYA NMR method.

Authors:  Mitsuhiro Takeda; Teppei Ikeya; Peter Güntert; Masatsune Kainosho
Journal:  Nat Protoc       Date:  2007       Impact factor: 13.491

7.  A computer-based protocol for semiautomated assignments and 3D structure determination of proteins.

Authors:  R P Meadows; E T Olejniczak; S W Fesik
Journal:  J Biomol NMR       Date:  1994-01       Impact factor: 2.835

8.  Bayesian signal extraction from noisy FT NMR spectra.

Authors:  A Rouh; A Louis-Joseph; J Y Lallemand
Journal:  J Biomol NMR       Date:  1994-07       Impact factor: 2.835

9.  Protein backbone angle restraints from searching a database for chemical shift and sequence homology.

Authors:  G Cornilescu; F Delaglio; A Bax
Journal:  J Biomol NMR       Date:  1999-03       Impact factor: 2.835

10.  Protein three-dimensional structure determination and sequence-specific assignment of 13C and 15N-separated NOE data. A novel real-space ab initio approach.

Authors:  P J Kraulis
Journal:  J Mol Biol       Date:  1994-11-04       Impact factor: 5.469

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  100 in total

1.  Simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space.

Authors:  Daniel Gottstein; Donata K Kirchner; Peter Güntert
Journal:  J Biomol NMR       Date:  2012-02-22       Impact factor: 2.835

2.  Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples.

Authors:  Oliver F Lange; Paolo Rossi; Nikolaos G Sgourakis; Yifan Song; Hsiau-Wei Lee; James M Aramini; Asli Ertekin; Rong Xiao; Thomas B Acton; Gaetano T Montelione; David Baker
Journal:  Proc Natl Acad Sci U S A       Date:  2012-06-25       Impact factor: 11.205

3.  SAGA: rapid automatic mainchain NMR assignment for large proteins.

Authors:  Gordon M Crippen; Aikaterini Rousaki; Matthew Revington; Yongbo Zhang; Erik R P Zuiderweg
Journal:  J Biomol NMR       Date:  2010-03-16       Impact factor: 2.835

4.  The Exact NOE as an Alternative in Ensemble Structure Determination.

Authors:  Beat Vögeli; Simon Olsson; Peter Güntert; Roland Riek
Journal:  Biophys J       Date:  2016-01-05       Impact factor: 4.033

5.  Advances in Nuclear Magnetic Resonance for Drug Discovery.

Authors:  Robert Powers
Journal:  Expert Opin Drug Discov       Date:  2009-10-01       Impact factor: 6.098

6.  Automated assignment of NMR chemical shifts using peak-particle dynamics simulation with the DYNASSIGN algorithm.

Authors:  Roland Schmucki; Shigeyuki Yokoyama; Peter Güntert
Journal:  J Biomol NMR       Date:  2008-11-26       Impact factor: 2.835

Review 7.  An introduction to biological NMR spectroscopy.

Authors:  Dominique Marion
Journal:  Mol Cell Proteomics       Date:  2013-07-06       Impact factor: 5.911

8.  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

9.  Exclusively NOESY-based automated NMR assignment and structure determination of proteins.

Authors:  Teppei Ikeya; Jun-Goo Jee; Yoshiki Shigemitsu; Junpei Hamatsu; Masaki Mishima; Yutaka Ito; Masatsune Kainosho; Peter Güntert
Journal:  J Biomol NMR       Date:  2011-03-30       Impact factor: 2.835

10.  The First structure of a lantibiotic immunity protein, SpaI from Bacillus subtilis, reveals a novel fold.

Authors:  Nina A Christ; Sophie Bochmann; Daniel Gottstein; Elke Duchardt-Ferner; Ute A Hellmich; Stefanie Düsterhus; Peter Kötter; Peter Güntert; Karl-Dieter Entian; Jens Wöhnert
Journal:  J Biol Chem       Date:  2012-08-17       Impact factor: 5.157

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