Comprehensive Strategy for Proton Chemical Shift Prediction: Linear Prediction with Nonlinear Corrections

2014 ◽  
Vol 54 (2) ◽  
pp. 419-430 ◽  
Author(s):  
Reino Laatikainen ◽  
Tommi Hassinen ◽  
Juuso Lehtivarjo ◽  
Mika Tiainen ◽  
Juha Jungman ◽  
...  
Keyword(s):  
Chemical Shift ◽  
Linear Prediction ◽  
Proton Chemical Shift ◽  
Comprehensive Strategy ◽  
Chemical Shift Prediction

NMR proton chemical shift prediction of C·C mismatches in B-DNA

2015 ◽  
Vol 252 ◽  
pp. 87-93 ◽  
Author(s):  
Kui Sang Ng ◽  
Sik Lok Lam
Keyword(s):  
Chemical Shift ◽  
Proton Chemical Shift ◽  
Chemical Shift Prediction

NMR proton chemical shift prediction of T·T mismatches in B-DNA duplexes

2013 ◽  
Vol 234 ◽  
pp. 184-189 ◽  
Author(s):  
Chun Kit Kwok ◽  
Sik Lok Lam
Keyword(s):  
Chemical Shift ◽  
Proton Chemical Shift ◽  
Dna Duplexes ◽  
Chemical Shift Prediction

Proton chemical shift prediction of A·A mismatches in B-DNA duplexes

2007 ◽  
Vol 187 (1) ◽  
pp. 105-111 ◽  
Author(s):  
Sik Lok Lam ◽  
Kin Fung Lai ◽  
Lai Man Chi
Keyword(s):  
Chemical Shift ◽  
Proton Chemical Shift ◽  
Dna Duplexes ◽  
Chemical Shift Prediction

Proton chemical-shift imaging with non-uniform fields

1986 ◽  
Vol 31 (10) ◽  
pp. 1101-1105 ◽  
Author(s):  
E Feig
Keyword(s):  
Chemical Shift ◽  
Chemical Shift Imaging ◽  
Proton Chemical Shift

ChemInform Abstract: COMBINED MULTIPLE PULSE NMR AND SAMPLE SPINNING: RECOVERY OF PROTON CHEMICAL SHIFT TENSORS

1980 ◽  
Vol 11 (11) ◽  
Author(s):  
R. E. TAYLOR ◽  
R. G. PEMBLETON ◽  
L. M. RYAN ◽  
B. C. GERSTEIN
Keyword(s):  
Chemical Shift ◽  
Proton Chemical Shift ◽  
Chemical Shift Tensors ◽  
Multiple Pulse

Proton Chemical Shift Tensors and Hydrogen Bond Geometry:  A1H−2H Dipolar NMR Study of the Water Molecule in Crystalline Hydrates

1998 ◽  
Vol 120 (50) ◽  
pp. 13187-13193 ◽  
Author(s):  
Gang Wu ◽  
Christopher J. Freure ◽  
Elodie Verdurand
Keyword(s):  
Hydrogen Bond ◽  
Chemical Shift ◽  
Water Molecule ◽  
Proton Chemical Shift ◽  
Chemical Shift Tensors ◽  
Nmr Study ◽  
Crystalline Hydrates

Temperature Imaging by Proton Chemical Shift

2020 ◽  
pp. 63-103
Author(s):  
Kagayaki Kuroda ◽  
Shiro Tsutsumi
Keyword(s):  
Chemical Shift ◽  
Proton Chemical Shift ◽  
Temperature Imaging

scholarly journals Protein structure refinement using a quantum mechanics-based chemical shielding predictor

2016 ◽  
Author(s):  
Lars A. Bratholm ◽  
Jan H. Jensen
Keyword(s):  
Quantum Mechanics ◽  
Simulated Annealing ◽  
Chemical Shift ◽  
Force Field ◽  
Chemical Shifts ◽  
Protein Structures ◽  
Empirical Methods ◽  
Structural Refinement ◽  
Chemical Shielding ◽  
Chemical Shift Prediction

The accurate prediction of protein chemical shifts using quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor of protein backbone and CB chemical shifts (ProCS15, PeerJ 2016, 3:e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic chemical shielding values (ProCS15) can be used to refine protein structures using Markov Chain Monte Carlo (MCMC) simulations, relating the chemical shielding values to the experimental chemical shifts probabilistically. Two kinds of MCMC structural refinement simulations were performed using force field geometry optimized X-ray structures as starting points: Simulated annealing of the starting structure and constant temperature MCMC simulation followed by simulated annealing of a representative ensemble structure. Annealing of the CHARMM structure changes the CA-RMSD by an average of 0.4 Å but lowers the chemical shift RMSD by 1.0 and 0.7 ppm for CA and N. Conformational averaging has a relatively small effect (0.1 - 0.2 ppm) on the overall agreement with carbon chemical shifts but lowers the error for nitrogen chemical shifts by 0.4 ppm. If a residue-specific offset is included the ProCS15 predicted chemical shifts have RMSD values relative to experiment that are comparable to popular empirical chemical shift predictors. The annealed representative ensemble structures differs in CA-RMSD relative to the initial structures by an average of 2.0 Å, with >2.0 Å difference for six proteins. In four of the cases, the largest structural differences arise in structurally flexible regions of the protein as determined by NMR, and in the remaining two cases, the large structural change may be due to force field deficiencies. The overall accuracy of the empirical methods are slightly improved by annealing the CHARMM structure with ProCS15, which may suggest that the minor structural changes introduced by ProCS15-based annealing improves the accuracy of the protein structures. Having established that QM-based chemical shift prediction can deliver the same accuracy as empirical shift predictors we hope this can help increase the accuracy of related approaches such as QM/MM or linear scaling approaches or interpreting protein structural dynamics from QM-derived chemical shift.

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