NMR-derived chemical shifts are structural fingerprints that are sensitive to the underlying conformational distributions of molecules. Thus, chemical shift data are now routinely used to infer the dynamical or conformational ensembles of peptides and proteins. However, for RNAs, techniques for inferring their conformational ensembles from chemical shift data have received less attention. Here, we used chemical shift data and the Bayesian/maximum entropy (BME) approach to model the secondary...
[NMR paper] Probabilistic validation of protein NMR chemical shift assignments.
Probabilistic validation of protein NMR chemical shift assignments.
Probabilistic validation of protein NMR chemical shift assignments.
J Biomol NMR. 2016 Jan 2;
Authors: Dashti H, Tonelli M, Lee W, Westler WM, Cornilescu G, Ulrich EL, Markley JL
Abstract
Data validation plays an important role in ensuring the reliability and reproducibility of studies. NMR investigations of the functional properties, dynamics, chemical kinetics, and structures of proteins depend critically on the correctness of chemical shift assignments....
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01-05-2016 08:23 PM
Probabilistic validation of protein NMR chemical shift assignments
Probabilistic validation of protein NMR chemical shift assignments
Abstract
Data validation plays an important role in ensuring the reliability and reproducibility of studies. NMR investigations of the functional properties, dynamics, chemical kinetics, and structures of proteins depend critically on the correctness of chemical shift assignments. We present a novel probabilistic method named ARECA for validating chemical shift assignments that relies on the nuclear Overhauser effect data . ARECA has been evaluated through its application to 26...
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01-03-2016 01:25 AM
[NMR paper] Using pseudocontact shifts and residual dipolar couplings as exact NMR restraints for the determination of protein structural ensembles.
Using pseudocontact shifts and residual dipolar couplings as exact NMR restraints for the determination of protein structural ensembles.
Using pseudocontact shifts and residual dipolar couplings as exact NMR restraints for the determination of protein structural ensembles.
Biochemistry. 2015 Dec 1;
Authors: Camilloni C, Vendruscolo M
Abstract
Nuclear magnetic resonance (NMR) spectroscopy provides detailed information about the struc-ture and dynamics of proteins by exploiting the conformational dependence of the magnetic...
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12-02-2015 11:37 AM
[NMR paper] Towards Relatively General and Accurate Quantum Chemical Predictions of Solid-State (17)O NMR Chemical Shifts in Various Biologically Relevant Oxygen-containing Compounds.
Towards Relatively General and Accurate Quantum Chemical Predictions of Solid-State (17)O NMR Chemical Shifts in Various Biologically Relevant Oxygen-containing Compounds.
Towards Relatively General and Accurate Quantum Chemical Predictions of Solid-State (17)O NMR Chemical Shifts in Various Biologically Relevant Oxygen-containing Compounds.
J Phys Chem B. 2015 Aug 14;
Authors: Rorick A, Michael MA, Yang L, Zhang Y
Abstract
Oxygen is an important element in most biologically significant molecules and experimental solid-state...
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08-15-2015 04:01 PM
PPM: a side-chain and backbone chemical shift predictor for the assessment of protein conformational ensembles
PPM: a side-chain and backbone chemical shift predictor for the assessment of protein conformational ensembles
Abstract The combination of the wide availability of protein backbone and side-chain NMR chemical shifts with advances in understanding of their relationship to protein structure makes these parameters useful for the assessment of structural-dynamic protein models. A new chemical shift predictor (PPM) is introduced, which is solely based on physicalâ??chemical contributions to the chemical shifts for both the protein backbone and methyl-bearing amino-acid side chains. To...
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09-15-2012 09:04 AM
RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts
RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts
Abstract The significant biological role of RNA has further highlighted the need for improving the accuracy, efficiency and the reach of methods for investigating RNA structure and function. Nuclear magnetic resonance (NMR) spectroscopy is vital to furthering the goals of RNA structural biology because of its distinctive capabilities. However, the dispersion pattern in the NMR spectra of RNA makes automated resonance assignment, a key step in NMR investigation of biomolecules, remarkably challenging. Herein we present RNA...
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02-27-2012 06:56 AM
Mapping of protein structural ensembles by chemical shifts
Abstract Applying the chemical shift prediction programs SHIFTX and SHIFTS to a data base of protein structures with known chemical shifts we show that the averaged chemical shifts predicted from the structural ensembles explain better the experimental data than the lowest energy structures. This is in agreement with the fact that proteins in solution occur in multiple conformational states in fast exchange on the chemical shift time scale. However, in contrast to the real conditions in solution at ambient temperatures, the standard NMR structural calculation methods as well chemical shift...
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08-14-2010 04:19 AM
A probabilistic approach for validating protein NMR chemical shift assignments
Abstract It has been estimated that more than 20% of the proteins in the BMRB are improperly referenced and that about 1% of all chemical shift assignments are mis-assigned. These statistics also reflect the likelihood that any newly assigned protein will have shift assignment or shift referencing errors. The relatively high frequency of these errors continues to be a concern for the biomolecular NMR community. While several programs do exist to detect and/or correct chemical shift mis-referencing or chemical shift mis-assignments, most can only do one, or the other. The one program...
Probabilistic Modeling of RNA Ensembles Using NMR Chemical Shifts
Linear Mode
