Abstract：
:A computer program has been developed to accurately and automatically predict the 1H and 13C chemical shifts of unassigned proteins on the basis of sequence homology. The program (called SHIFTY) uses standard sequence alignment techniques to compare the sequence of an unassigned protein against the BioMagResBank--a public database containing sequences and NMR chemical shifts of nearly 200 assigned proteins [Seavey et al. (1991) J Biomol. NMR, 1, 217-236]. From this initial sequence alignment, the program uses a simple set of rules to directly assign or transfer a complete set of 1H or 13C chemical shifts (from the previously assigned homologues) to the unassigned protein. This 'homologous assignment' protocol takes advantage of the simple fact that homologous proteins tend to share both structural similarity and chemical shift similarity. SHIFTY has been extensively tested on more than 25 medium-sized proteins. Under favorable circumstances, this program can predict the 1H or 13C chemical shifts of proteins with an accuracy far exceeding any other method published to date. With the exponential growth in the number of assigned proteins appearing in the literature (now at a rate of more than 150 per year), we believe that SHIFTY may have widespread utility in assigning individual members in families of related proteins, an endeavor that accounts for a growing portion of the protein NMR work being done today.
journal_name
J Biomol NMRjournal_title
Journal of biomolecular NMRauthors
Wishart DS,Watson MS,Boyko RF,Sykes BDdoi
10.1023/a:1018373822088subject
Has Abstractpub_date
1997-12-01 00:00:00pages
329-36issue
4eissn
0925-2738issn
1573-5001journal_volume
10pub_type
杂志文章abstract：:We have developed an approach for simultaneous structure calculation and automatic Nuclear Overhauser Effect (NOE) assignment to solve nuclear magnetic resonance (NMR) structures from unassigned NOESY data. The approach, autoNOE-Rosetta, integrates Resolution Adapted Structural RECombination (RASREC) Rosetta NMR calcu...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-014-9833-3
更新日期：2014-07-01 00:00:00
abstract：:Activated dynamics plays a central role in protein function, where transitions between distinct conformations often underlie the switching between active and inactive states. The characteristic time scales of these transitions typically fall in the microsecond to millisecond range, which is amenable to investigations ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-013-9764-4
更新日期：2013-09-01 00:00:00
abstract：:Simple pulse schemes are presented for the measurement of methyl (13)C and (1)H CSA values from (1)H-(13)C dipole/(13)C CSA and (1)H-(13)C dipole/(1)H CSA cross-correlated relaxation. The methodology is applied to protein L and malate synthase G. Average (13)C CSA values are considerably smaller for Ile than Leu/Val (...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-004-4349-x
更新日期：2004-12-01 00:00:00
abstract：:We describe a general computational approach to site-specific resonance assignments in multidimensional NMR studies of uniformly (15)N,(13)C-labeled biopolymers, based on a simple Monte Carlo/simulated annealing (MCSA) algorithm contained in the program MCASSIGN2. Input to MCASSIGN2 includes lists of multidimensional ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-011-9517-1
更新日期：2011-07-01 00:00:00
abstract：:A three-dimensional 1H, 13C, 31P triple resonance experiment, HCP-CCH-TOCSY, is presented which provides unambiguous through-bond correlation of all 1H ribose protons on the 5' and 3' sides of the intervening phosphorus along the backbone bonding network in 13C-labeled RNA oligonucleotides. The correlation of the comp...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF00227473
更新日期：1995-01-01 00:00:00
abstract：:A major difficulty in determining the structure of an oligomeric protein by NMR is the problem of distinguishing inter- from intraprotomer NOEs. In order to address this issue in studies of the 27 kD compact trimeric domain of the MHC class II-associated invariant chain, we compared the 13C NOESY-HSQC spectrum of a un...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1008285512845
更新日期：1998-08-01 00:00:00
abstract：:Insights into the structure and dynamics of large biological systems has been greatly improved by two concurrent NMR approaches: the application of transverse relaxation-optimized spectroscopy (TROSY) techniques in multi-dimensional NMR, especially the methyl-TROSY, and the resurgence of 19F NMR using trifluoromethyl ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-019-00266-0
更新日期：2019-11-01 00:00:00
abstract：:Active bandwidth and global quality factor are the two main metrics used to quantitatively compare the performance of TOCSY mixing sequences. Active bandwidth refers to the spectral region over which at least 50 % of the magnetization is transferred via a coupling. Global quality factor scores mixing sequences accordi...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-016-0051-z
更新日期：2016-09-01 00:00:00
abstract：:We have developed an improved isotope-filtered pulse scheme in combination with a double-tuned filter, a hyperbolic secant inversion pulse, and a z-filter with a pulsed field gradient. These filtering pulse schemes have been incorporated into several one-, two-, and three-dimensional experiments, which were applied to...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF00228150
更新日期：1996-12-01 00:00:00
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journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-017-0141-6
更新日期：2017-10-01 00:00:00
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journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-015-9909-8
更新日期：2015-05-01 00:00:00
abstract：:A comparison is made of the consequences of using time-averaged and conventional vicinal (3)J-coupling restraints in molecular dynamics refinement of an adenosine nucleoside model system. The target values for the restraints are derived from a 3-ns unrestrained molecular dynamics simulation. A comparison of the result...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF00175253
更新日期：1994-03-01 00:00:00
abstract：:An approach to the determination of the 2-(13)C' chemical shift (CS) tensor orientation in pyrimidine bases via heteronuclear MAS NMR spectroscopy is presented. Considering a dipolar coupled spin 1/2 network of the type S1-I-S2 consisting of directly bonded heteronuclear spins, we have carried out numerical simulation...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1008318530946
更新日期：2000-10-01 00:00:00
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journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-018-0173-6
更新日期：2018-04-01 00:00:00
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journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-005-8872-1
更新日期：2005-08-01 00:00:00
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journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF00211775
更新日期：1995-09-01 00:00:00
abstract：:A pulse sequence is described for recording single-quantum (13)C-methyl relaxation dispersion profiles of (13)C-selectively labeled methyl groups in proteins that offers significant improvements in sensitivity relative to existing approaches where initial magnetization derives from (13)C polarization. Sensitivity gain...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-007-9149-7
更新日期：2007-05-01 00:00:00
abstract：:The importance of protein chemical shift values for the determination of three-dimensional protein structure has increased in recent years because of the large databases of protein structures with assigned chemical shift data. These databases have allowed the investigation of the quantitative relationship between chem...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1023060720156
更新日期：2003-05-01 00:00:00
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journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-020-00354-6
更新日期：2021-01-27 00:00:00
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journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-017-0109-6
更新日期：2017-04-01 00:00:00
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journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-006-0029-3
更新日期：2006-06-01 00:00:00
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journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-012-9683-9
更新日期：2013-01-01 00:00:00
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journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-013-9776-0
更新日期：2013-10-01 00:00:00
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journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-010-9417-9
更新日期：2010-06-01 00:00:00
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journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-016-0044-y
更新日期：2016-08-01 00:00:00
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journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-016-0017-1
更新日期：2016-02-01 00:00:00
abstract：:In aqueous solution, exchanging peptide NH protons experience two environments, that of the peptide itself with a relatively slow diffusion coefficient and that of the water solvent with a faster diffusion coefficient. Although in slow exchange on the NMR chemical shift timescale, the magnetic field gradient dependenc...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/A:1008393202076
更新日期：1999-01-01 00:00:00
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journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF01875522
更新日期：1991-09-01 00:00:00
abstract：:Post-translationally modified proteins make up the majority of the proteome and establish, to a large part, the impressive level of functional diversity in higher, multi-cellular organisms. Most eukaryotic post-translational protein modifications (PTMs) denote reversible, covalent additions of small chemical entities ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-012-9674-x
更新日期：2012-11-01 00:00:00
abstract：:The solution molecular structure of the four-iron ferredoxin (Fd) from the hyperthermophilic archaeon Thermococcus litoralis (Tl) has been investigated by 1H NMR spectroscopy. TOCSY and NOESY experiments in H2O, tailored to detect both weakly and strongly relaxed resonances, together with steady-state NOEs in both H2O...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF00190455
更新日期：1996-01-01 00:00:00
