Related ArticlesComputer-assisted assignment of 2D 1H NMR spectra of proteins: basic algorithms and application to phoratoxin B.
J Biomol NMR. 1991 May;1(1):23-47
Authors: Kleywegt GJ, Boelens R, Cox M, Llinás M, Kaptein R
A suite of computer programs (CLAIRE) is described which can be of assistance in the process of assigning 2D 1H NMR spectra of proteins. The programs embody a software implementation of the sequential assignment approach first developed by Wüthrich and co-workers (K. Wüthrich, G. Wider, G. Wagner and W. Braun (1982) J. Mol. Biol. 155, 311). After data-abstraction (peakpicking), the software can be used to detect patterns (spin systems), to find cross peaks between patterns in 2D NOE data sets and to generate assignments that are consistent with all available data and which satisfy a number of constraints imposed by the user. An interactive graphics program called CONPAT is used to control the entire assignment process as well as to provide the essential feedback from the experimental NMR spectra. The algorithms are described in detail and the approach is demonstrated on a set of spectra from the mistletoe protein phoratoxin B, a homolog of crambin. The results obtained compare well with those reported earlier based entirely on a manual assignment process.
New Book on Computer-Assisted Structure Elucidation
Source: Ryan's blog
New Book on Computer-Assisted Structure Elucidation
It's been a very long time since my last post. I apologize for that, but I can assure that my posting absence has not been due to lack of quality things to talk about. Hopefully this post will help me...
Read more...
nmrlearner
Books
0
02-15-2012 04:01 PM
New Book on Computer-Assisted Structure Elucidation
Source: Ryan's blog
New Book on Computer-Assisted Structure Elucidation
It's been a very long time since my last post. I apologize for that, but I can assure that my posting absence has not been due to lack of quality things to talk about. Hopefully this post will help me...
Read more...
nmrlearner
Books
0
02-15-2012 03:51 PM
[NMR paper] Reconsidering complete search algorithms for protein backbone NMR assignment.
Reconsidering complete search algorithms for protein backbone NMR assignment.
Related Articles Reconsidering complete search algorithms for protein backbone NMR assignment.
Bioinformatics. 2005 Sep 1;21 Suppl 2:ii230-6
Authors: Vitek O, Bailey-Kellogg C, Craig B, Kuliniewicz P, Vitek J
MOTIVATION: Nuclear magnetic resonance (NMR) spectroscopy is widely used to determine and analyze protein structures. An essential step in NMR studies is determining the backbone resonance assignment, which maps individual atoms to experimentally measured...
nmrlearner
Journal club
0
12-01-2010 06:56 PM
[NMR paper] Mass spectrometry assisted assignment of NMR resonances in 15N labeled proteins.
Mass spectrometry assisted assignment of NMR resonances in 15N labeled proteins.
Related Articles Mass spectrometry assisted assignment of NMR resonances in 15N labeled proteins.
J Am Chem Soc. 2004 Nov 10;126(44):14377-9
Authors: Feng L, Orlando R, Prestegard JH
Application of nuclear magnetic resonance (NMR) methods for the structural characterization to larger and more complex protein systems can be facilitated through the development of new methods for resonance assignment. Here, a novel approach that relies on integration of NMR and mass...
nmrlearner
Journal club
0
11-24-2010 10:03 PM
[NMR paper] Resonance assignment strategies for the analysis of NMR spectra of proteins.
Resonance assignment strategies for the analysis of NMR spectra of proteins.
Related Articles Resonance assignment strategies for the analysis of NMR spectra of proteins.
Mol Biotechnol. 1994 Aug;2(1):61-93
Authors: Leopold MF, Urbauer JL, Wand AJ
Determination of the high resolution solution structure of a protein using nuclear magnetic resonance (NMR) spectroscopy requires that resonances observed in the NMR spectra be unequivocally assigned to individual nuclei of the protein. With the advent of modern, two-dimensional NMR techniques arose...
nmrlearner
Journal club
0
08-22-2010 03:29 AM
[NMR paper] Sequential assignment of 2D-NMR spectra of proteins using genetic algorithms.
Sequential assignment of 2D-NMR spectra of proteins using genetic algorithms.
Related Articles Sequential assignment of 2D-NMR spectra of proteins using genetic algorithms.
J Chem Inf Comput Sci. 1993 Mar-Apr;33(2):245-51
Authors: Wehrens R, Lucasius C, Buydens L, Kateman G
The application of genetic algorithms to the problem of the sequential assignment of two-dimensional protein NMR spectra is discussed. The problem is heavily underconstrained since in most cases more patterns are available than amino acid positions, and uncertainties may...
nmrlearner
Journal club
0
08-21-2010 11:53 PM
[NMR paper] A novel approach for sequential assignment of 1H, 13C, and 15N spectra of proteins: h
A novel approach for sequential assignment of 1H, 13C, and 15N spectra of proteins: heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin.
Related Articles A novel approach for sequential assignment of 1H, 13C, and 15N spectra of proteins: heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin.
Biochemistry. 1990 May 15;29(19):4659-67
Authors: Ikura M, Kay LE, Bax A
A novel approach is described for obtaining sequential assignment of the backbone 1H, 13C, and 15N...
nmrlearner
Journal club
0
08-21-2010 10:48 PM
[NMR paper] Assignment strategies in homonuclear three-dimensional 1H NMR spectra of proteins.
Assignment strategies in homonuclear three-dimensional 1H NMR spectra of proteins.
Related Articles Assignment strategies in homonuclear three-dimensional 1H NMR spectra of proteins.
Biochemistry. 1990 Feb 20;29(7):1829-39
Authors: Vuister GW, Boelens R, Padilla A, Kleywegt GJ, Kaptein R
The increase in dimensionality of three-dimensional (3D) NMR greatly enhances the spectral resolution in comparison to 2D NMR. It alleviates the problem of resonance overlap and may extend the range of molecules amenable to structure determination by...