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Literature DB >> 19234673

Chemical shift optimization in multidimensional NMR spectra by AUREMOL-SHIFTOPT.

Kumaran Baskaran¹, Renate Kirchhöfer, Fritz Huber, Jochen Trenner, Konrad Brunner, Wolfram Gronwald, Klaus-Peter Neidig, Hans Robert Kalbitzer.

Abstract

A problem often encountered in multidimensional NMR-spectroscopy is that an existing chemical shift list of a protein has to be used to assign an experimental spectrum but does not fit sufficiently well for a safe assignment. A similar problem occurs when temperature or pressure series of n-dimensional spectra are to be evaluated automatically. We have developed two different algorithms, AUREMOL-SHIFTOPT1 and AUREMOL-SHIFTOPT2 that fulfill this task. In the present contribution their performance is analyzed employing a set of simulated and experimental two-dimensional and three-dimensional spectra obtained from three different proteins. A new z-score based on atom and amino acid specific chemical shift distributions is introduced to weight the chemical shift contributions in different dimensions properly.

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Year: 2009 PMID： 19234673 DOI： 10.1007/s10858-009-9304-4

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

16 in total

1. Automatic assignment of NOESY cross peaks and determination of the protein structure of a new world scorpion neurotoxin using NOAH/DIAMOD.

Authors: Y Xu; M J Jablonsky; P L Jackson; W Braun; N R Krishna
Journal: J Magn Reson Date: 2001-01 Impact factor: 2.229

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. Combined chemical shift changes and amino acid specific chemical shift mapping of protein-protein interactions.

Authors: Frank H Schumann; Hubert Riepl; Till Maurer; Wolfram Gronwald; Klaus-Peter Neidig; Hans Robert Kalbitzer
Journal: J Biomol NMR Date: 2007-10-23 Impact factor: 2.835

5. Structure of the leech protein saratin and characterization of its binding to collagen.

Authors: Wolfram Gronwald; Jörg Bomke; Till Maurer; Barbara Domogalla; Fritz Huber; Frank Schumann; Werner Kremer; Florian Fink; Thomas Rysiok; Matthias Frech; Hans Robert Kalbitzer
Journal: J Mol Biol Date: 2008-06-18 Impact factor: 5.469

6. Use of global symmetries in automated signal class recognition by a bayesian method

Authors:
Journal: J Magn Reson Date: 1997-12 Impact factor: 2.229

7. Automated analysis of protein NMR assignments using methods from artificial intelligence.

Authors: D E Zimmerman; C A Kulikowski; Y Huang; W Feng; M Tashiro; S Shimotakahara; C Chien; R Powers; G T Montelione
Journal: J Mol Biol Date: 1997-06-20 Impact factor: 5.469

8. A general Bayesian method for an automated signal class recognition in 2D NMR spectra combined with a multivariate discriminant analysis.

Authors: C Antz; K P Neidig; H R Kalbitzer
Journal: J Biomol NMR Date: 1995-04 Impact factor: 2.835