The automated assignment of NOESY cross peaks has become a fundamental technique for NMR protein structure analysis. A widely used algorithm for this purpose is implemented in the program CYANA. It has been used for a large number of structure determinations of proteins in solution but was so far not described in full detail. In this paper we present a complete description of the CYANA implementation of automated NOESY assignment, which differs extensively from its predecessor CANDID by the use of a consistent probabilistic treatment, and we discuss its performance in the second round of the critical assessment of structure determination by NMR.
Systematic evaluation of combined automated NOE assignment and structure calculation with CYANA
Systematic evaluation of combined automated NOE assignment and structure calculation with CYANA
Abstract
The automated assignment of NOESY cross peaks has become a fundamental technique for NMR protein structure analysis. A widely used algorithm for this purpose is implemented in the program CYANA. It has been used for a large number of structure determinations of proteins in solution but a systematic evaluation of its performance has not yet been reported. In this paper we systematically analyze the reliability of combined automated NOESY assignment...
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Exclusively NOESY-based automated NMR assignment and structure determination of proteins
Exclusively NOESY-based automated NMR assignment and structure determination of proteins
Abstract A fully automated method is presented for determining NMR solution structures of proteins using exclusively NOESY spectra as input, obviating the need to measure any spectra only for obtaining resonance assignments but devoid of structural information. Applied to two small proteins, the approach yielded structures that coincided closely with conventionally determined structures.
Content Type Journal Article
Pages 1-10
DOI 10.1007/s10858-011-9502-8
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04-01-2011 09:31 PM
Exclusively NOESY-based automated NMR assignment and structure determination of proteins.
Exclusively NOESY-based automated NMR assignment and structure determination of proteins.
Exclusively NOESY-based automated NMR assignment and structure determination of proteins.
J Biomol NMR. 2011 Mar 30;
Authors: Ikeya T, Jee JG, Shigemitsu Y, Hamatsu J, Mishima M, Ito Y, Kainosho M, Güntert P
A fully automated method is presented for determining NMR solution structures of proteins using exclusively NOESY spectra as input, obviating the need to measure any spectra only for obtaining resonance assignments but devoid of structural information....
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03-31-2011 06:24 PM
Error tolerant NMR backbone resonance assignment and automated structure generation.
Error tolerant NMR backbone resonance assignment and automated structure generation.
Error tolerant NMR backbone resonance assignment and automated structure generation.
J Bioinform Comput Biol. 2011 Feb;9(1):15-41
Authors: Alipanahi B, Gao X, Karakoc E, Li SC, Balbach F, Feng G, Donaldson L, Li M
Error tolerant backbone resonance assignment is the cornerstone of the NMR structure determination process. Although a variety of assignment approaches have been developed, none works sufficiently well on noisy fully automatically picked peaks to enable...
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02-18-2011 08:07 PM
[NMR paper] Automated NMR structure calculation with CYANA.
Automated NMR structure calculation with CYANA.
Related Articles Automated NMR structure calculation with CYANA.
Methods Mol Biol. 2004;278:353-78
Authors: Güntert P
This chapter gives an introduction to automated nuclear magnetic resonance (NMR) structure calculation with the program CYANA. Given a sufficiently complete list of assigned chemical shifts and one or several lists of cross-peak positions and columns from two-, three-, or four-dimensional nuclear Overhauser effect spectroscopy (NOESY) spectra, the assignment of the NOESY...
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11-24-2010 09:25 PM
[NMR paper] Protein NMR structure determination with automated NOE assignment using the new softw
Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.
Related Articles Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.
J Mol Biol. 2002 May 24;319(1):209-27
Authors: Herrmann T, Güntert P, Wüthrich K
Combined automated NOE assignment and structure determination module (CANDID) is a new software for efficient NMR structure determination of proteins by automated...
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11-24-2010 08:49 PM
[NMR paper] The NOESY jigsaw: automated protein secondary structure and main-chain assignment fro
The NOESY jigsaw: automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data.
Related Articles The NOESY jigsaw: automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data.
J Comput Biol. 2000;7(3-4):537-58
Authors: Bailey-Kellogg C, Widge A, Kelley JJ, Berardi MJ, Bushweller JH, Donald BR
High-throughput, data-directed computational protocols for Structural Genomics (or Proteomics) are required in order to evaluate the protein products of genes for structure and...
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11-18-2010 09:15 PM
PASD: auto NOE assignment & structure calculation
Completely Automated, Highly Error-Tolerant Macromolecular Structure Determination from Multidimensional Nuclear Overhauser Enhancement Spectra and Chemical Shift Assignments
Kuszewski, J.; Schwieters, C. D.; Garrett, D. S.; Byrd, R. A.; Tjandra, N.; Clore, G. M.;
J. Am. Chem. Soc. 2004; 126(20); 6258-6273
http://pubs.acs.org/isubscribe/journals/jacsat/126/i20/figures/ja049786hn00001.gif
Abstract:
The major rate-limiting step in high-throughput NMR protein structure determination involves the calculation of a reliable initial fold, the elimination of incorrect nuclear Overhauser...
Combined automated NOE assignment and structure calculation with CYANA
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