Related ArticlesHistogram-based scoring schemes for protein NMR resonance assignment.
J Bioinform Comput Biol. 2004 Dec;2(4):747-64
Authors: Wan X, Tegos T, Lin G
In NMR protein structure determination, after the resonance peaks have been identified and chemical shifts from peaks across multiple spectra have been grouped into spin systems, associating these spin systems to their host residues is the key toward the success of structural information extraction and thus the key to the success of the structure calculation. To achieve accurate enough structure calculation, a near complete and accurate assignment is a prerequisite. There are two pieces of information that can be used into the assignment, one of which is the adjacency information among the spin systems and the other is the signature information of the spin systems. The signature information reflects the fact that, generally speaking, for one type of amino acid residing in a specific local structural environment, the chemical shifts for the atoms inside the amino acid fall into some very narrow distinct ranges. In most of the existing work, normal distributions are assumed with means and standard deviations statistically collected from the available data. In this paper, we followed a simple yet effective histogram-based way to estimate for every spin system the probability that its host is a certain type of amino acid residing in a certain type of secondary structure. We used two combinations of chemical shifts to demonstrate the effectiveness of this type of histogram-based scoring schemes.
An NMR-based scoring function improves the accuracy of binding pose predictions by docking by two orders of magnitude
An NMR-based scoring function improves the accuracy of binding pose predictions by docking by two orders of magnitude
Abstract Low-affinity ligands can be efficiently optimized into high-affinity drug leads by structure based drug design when atomic-resolution structural information on the protein/ligand complexes is available. In this work we show that the use of a few, easily obtainable, experimental restraints improves the accuracy of the docking experiments by two orders of magnitude. The experimental data are measured in nuclear magnetic resonance spectra and consist of...
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12-17-2011 04:44 AM
Chemical shift correlation at high MAS frequencies employing low-power symmetry-based mixing schemes
Chemical shift correlation at high MAS frequencies employing low-power symmetry-based mixing schemes
Abstract An approach for conveniently implementing low-power CN n ν and RN n ν symmetry-based band-selective mixing sequences for generating homo- and heteronuclear chemical shift correlation NMR spectra of low γ nuclei in biological solids is demonstrated. Efficient magnetisation transfer characteristics are achieved by selecting appropriate symmetries requiring the application of basic RF elements of relatively long duration and numerically tailoring the RF field modulation profile...
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06-20-2011 03:31 PM
[NMR paper] GFT NMR based resonance assignment for the 21 kDa human protein UFC1.
GFT NMR based resonance assignment for the 21 kDa human protein UFC1.
Related Articles GFT NMR based resonance assignment for the 21 kDa human protein UFC1.
J Biomol NMR. 2005 Jul;32(3):261
Authors: Liu G, Aramini J, Atreya HS, Eletsky A, Xiao R, Acton T, Ma L, Montelione GT, Szyperski T
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12-01-2010 06:56 PM
[NMR paper] Resonance assignment of proteins with high shift degeneracy based on 5D spectral info
Resonance assignment of proteins with high shift degeneracy based on 5D spectral information encoded in G2FT NMR experiments.
Related Articles Resonance assignment of proteins with high shift degeneracy based on 5D spectral information encoded in G2FT NMR experiments.
J Am Chem Soc. 2005 Apr 6;127(13):4554-5
Authors: Atreya HS, Eletsky A, Szyperski T
A suite of novel (5,3)D G2FT triple resonance NMR experiments encoding highly resolved 5D spectral information is presented for sequential resonance assignment of proteins exhibiting high chemical...
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11-25-2010 08:21 PM
[NMR paper] A modified strategy for sequence specific assignment of protein NMR spectra based on
A modified strategy for sequence specific assignment of protein NMR spectra based on amino acid type selective experiments.
Related Articles A modified strategy for sequence specific assignment of protein NMR spectra based on amino acid type selective experiments.
J Biomol NMR. 2005 Feb;31(2):115-28
Authors: Schubert M, Labudde D, Leitner D, Oschkinat H, Schmieder P
The determination of the three-dimensional structure of a protein or the study of protein-ligand interactions requires the assignment of all relevant nuclei as an initial step....
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11-24-2010 11:14 PM
13C-direct detected NMR experiments for the sequential J-based resonance assignment o
Abstract We present here a set of 13C-direct detected NMR experiments to facilitate the resonance assignment of RNA oligonucleotides. Three experiments have been developed: (1) the (H)CC-TOCSY-experiment utilizing a virtual decoupling scheme to assign the intraresidual ribose 13C-spins, (2) the (H)CPC-experiment that correlates each phosphorus with the C4â?² nuclei of adjacent nucleotides via J(C,P) couplings and (3) the (H)CPC-CCH-TOCSY-experiment that correlates the phosphorus nuclei with the respective C1â?²,H1â?² ribose signals. The experiments were applied to two RNA hairpin structures....
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08-14-2010 04:19 AM
Broadband 15Nâ??13C dipolar recoupling via symmetry-based RF pulse schemes at high MA
Abstract An approach for generating efficient
RNnnS, nk symmetry-based dual channel RF pulse schemes for γ-encoded broadband 15Nâ??13C dipolar recoupling at high magic angle spinning frequencies is presented. The method involves the numerical optimisation of the RF phase-modulation profile of the basic â??Râ?? element so as to obtain heteronuclear double quantum dipolar recoupling sequences with satisfactory magnetisation transfer characteristics. The basic â??Râ?? element was implemented as a sandwich of a small number of short pulses of equal duration with each pulse characterised by...
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08-14-2010 04:19 AM
Robust structure-based resonance assignment for functional protein studies by NMR
Abstract High-throughput functional protein NMR studies, like protein interactions or dynamics, require an automated approach for the assignment of the protein backbone. With the availability of a growing number of protein 3D structures, a new class of automated approaches, called structure-based assignment, has been developed quite recently. Structure-based approaches use primarily NMR input data that are not based on J-coupling and for which connections between residues are not limited by through bonds magnetization transfer efficiency. We present here a robust structure-based assignment...
Histogram-based scoring schemes for protein NMR resonance assignment.
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