Toward automated assignment of nuclear magnetic resonance spectra:  pattern recognition in two-dimensional correlation spectra

Pfaendler, Peter; Bodenhausen, Geoffrey; Meier, Beat; Ernst, R. R.

doi:10.1021/ac00290a018

Cited by 92 publications

(20 citation statements)

References 35 publications

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“…The complete automation of protein structure determination is one of the challenges of biomolecular NMR spectroscopy that has, despite early optimism [46], proved difficult to achieve. The unavoidable imperfections of experimental NMR spectra and the intrinsic ambiguity of peak assignments that results from the limited accuracy of frequency measurements turn the tractable problem of finding the chemical shift assignments from ideal spectra into a formidably difficult one under realistic conditions.…”

Section: Historical Developmentmentioning

confidence: 99%

“…The unavoidable imperfections of experimental NMR spectra and the intrinsic ambiguity of peak assignments that results from the limited accuracy of frequency measurements turn the tractable problem of finding the chemical shift assignments from ideal spectra into a formidably difficult one under realistic conditions. Many attempts have been made to automate further parts of the structure determination process, including peak identification [46][47][48][49][50][51][52][53][54][55][56][57][58][59][60], and the sequence-specific assignment of the chemical shifts . However, fully automated NMR structure determination was more demanding than automating individual parts of NMR structure analysis because the cumulative effect of imperfections at successive steps could easily render the overall process unsuccessful ( Figure 5.2).…”

Section: Historical Developmentmentioning

confidence: 99%

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Calculation of Structures from NMR Restraints

Güntert

2011

Protein NMR Spectroscopy: Practical Techniques and Applications

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When the NMR method for protein structure determination was introduced in the early 1980s the new approach met with enthusiasm amongst NMR spectroscopists, as well as scepticism and disbelief by structural biologists until the simultaneous but independent determinations of the three-dimensional structure of the protein tendamistat by X-ray crystallography [1] and NMR spectroscopy [2,3] yielded virtually identical results [4]. Since that time, NMR has become a firmly established method for determining the threedimensional structures of proteins. More than 7800 structures in the Protein Data Bank [5] of March 2009 have been determined by NMR ( Figure 5.1). This remarkable achievement would not have been possible without the development of sophisticated computational methods to compute three-dimensional protein structures from NMR-derived conformational restraints, and by increasingly automated approaches for analysing multidimensional NMR spectra.NMR structure calculations can be performed in several ways that differ essentially by the extent to which the analysis of the spectra is automated. In a basic structure calculation, all spectra are analysed by the spectroscopist who also interprets the data and provides the structure calculation program with geometric restraints in the form of allowed interatomic distance ranges, ranges of allowed torsion angle values, and Protein NMR Spectroscopy: Practical Techniques and Applications, First Edition. Edited

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Section: Historical Developmentmentioning

confidence: 99%

Section: Historical Developmentmentioning

confidence: 99%

Calculation of Structures from NMR Restraints

Güntert

2011

Protein NMR Spectroscopy: Practical Techniques and Applications

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“…For a discussion of the first of these four steps we refer to Kleywegt et al (1990) and the references cited therein. There have been several reports on programs which basically or exclusively tackle the problem of pattern detection on the basis of, usually, COSY, RELAY and/or HOHAHA spectra (Meier et al, 1984(Meier et al, , 1987Neidig et al, 1984;Pf'~indler et al, 1985;Weber et al, 1989). The program of Billeter et al (1988) deals with the final assignment step (assuming that the user has somehow accomplished the preceding tasks) in combination with extensive bookkeeping and consistency checking.…”

Section: Introductionmentioning

confidence: 99%

Computer-assisted assignment of 2D1H NMR spectra of proteins: Basic algorithms and application to phoratoxin B

et al. 1991

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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.

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“…At this level all crosspeaks appear as the basic quartet pattern since the secondary couplings have been largely removed by dilution. Besides providing ready determination of coupling constants the simplified crosspeak pattern should prove exceedingly valuable for automated pattern recognition analysis [5,6].…”

Section: Introductionmentioning

confidence: 99%

Chiral β and random fractional deuteration for the determination of protein sidechain conformation by NMR

LeMaster

1987

FEBS Letters

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Stereospecific assignments of the aspartic acid and asparagine fl-protons of the 108 residue protein E. coli thioredoxin have been obtained by the use of chiral deuteration. In addition protein samples have been prepared in which all carbon bound hydrogen positions are substituted to an extent of 75% with deuterium. These random fractionally deuterated samples significantly facilitate the measurement of coupling constants and intraresidue NOE intensities which combined with the stereospecific assignments have provided determination of the first sidechain dihedral angle Z1 for all four asparagine residues and eight of the ten assigned aspartic acid residues.

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Toward automated assignment of nuclear magnetic resonance spectra: pattern recognition in two-dimensional correlation spectra

Cited by 92 publications

References 35 publications

Calculation of Structures from NMR Restraints

Calculation of Structures from NMR Restraints

Computer-assisted assignment of 2D1H NMR spectra of proteins: Basic algorithms and application to phoratoxin B

Chiral β and random fractional deuteration for the determination of protein sidechain conformation by NMR

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