Literature DB >> 15465314

Automation of NMR structure determination of proteins.

Amanda S Altieri1, R Andrew Byrd.   

Abstract

The automation of protein structure determination using NMR is coming of age. The tedious processes of resonance assignment, followed by assignment of NOE (nuclear Overhauser enhancement) interactions (now intertwined with structure calculation), assembly of input files for structure calculation, intermediate analyses of incorrect assignments and bad input data, and finally structure validation are all being automated with sophisticated software tools. The robustness of the different approaches continues to deal with problems of completeness and uniqueness; nevertheless, the future is very bright for automation of NMR structure generation to approach the levels found in X-ray crystallography. Currently, near completely automated structure determination is possible for small proteins, and the prospect for medium-sized and large proteins is good. Copyright 2004 Elsevier Ltd.

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Year:  2004        PMID: 15465314     DOI: 10.1016/j.sbi.2004.09.003

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  20 in total

1.  Covariance NMR in higher dimensions: application to 4D NOESY spectroscopy of proteins.

Authors:  David A Snyder; Fengli Zhang; Rafael Brüschweiler
Journal:  J Biomol NMR       Date:  2007-09-18       Impact factor: 2.835

2.  KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies.

Authors:  Naohiro Kobayashi; Junji Iwahara; Seizo Koshiba; Tadashi Tomizawa; Naoya Tochio; Peter Güntert; Takanori Kigawa; Shigeyuki Yokoyama
Journal:  J Biomol NMR       Date:  2007-07-18       Impact factor: 2.835

3.  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

4.  Automated amino acid side-chain NMR assignment of proteins using (13)C- and (15)N-resolved 3D [ (1)H, (1)H]-NOESY.

Authors:  Francesco Fiorito; Torsten Herrmann; Fred F Damberger; Kurt Wüthrich
Journal:  J Biomol NMR       Date:  2008-08-16       Impact factor: 2.835

5.  Automated protein structure calculation from NMR data.

Authors:  Mike P Williamson; C Jeremy Craven
Journal:  J Biomol NMR       Date:  2009-01-10       Impact factor: 2.835

6.  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

Review 7.  Automated structure determination from NMR spectra.

Authors:  Peter Güntert
Journal:  Eur Biophys J       Date:  2008-09-20       Impact factor: 1.733

8.  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

9.  TSAR: a program for automatic resonance assignment using 2D cross-sections of high dimensionality, high-resolution spectra.

Authors:  Anna Zawadzka-Kazimierczuk; Wiktor Koźmiński; Martin Billeter
Journal:  J Biomol NMR       Date:  2012-07-18       Impact factor: 2.835

10.  PICKY: a novel SVD-based NMR spectra peak picking method.

Authors:  Babak Alipanahi; Xin Gao; Emre Karakoc; Logan Donaldson; Ming Li
Journal:  Bioinformatics       Date:  2009-06-15       Impact factor: 6.937

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