We mined the most recent editions of the BioMagResDataBank and the protein data bank to parametrize a new empirical knowledge-based chemical shift predictor of protein backbone atoms using either a linear or an artificial neural network model. The resulting chemical shift predictor PPM_One accepts a single static 3D structure as input and emulates the effect of local protein dynamics via interatomic steric contacts. Furthermore, the chemical shift prediction was extended to most side-chain protons and it is found that the prediction accuracy is at a level allowing an independent assessment of stereospecific assignments. For a previously established set of test proteins some overall improvement was achieved over current top-performing chemical shift prediction programs.
[NMR paper] Reliable resonance assignments of selected residues of proteins with known structure based on empirical NMR chemical shift prediction.
Reliable resonance assignments of selected residues of proteins with known structure based on empirical NMR chemical shift prediction.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Reliable resonance assignments of selected residues of proteins with known structure based on empirical NMR chemical shift prediction.
J Magn Reson. 2015 Mar 7;254:93-97
Authors: Li DW, Meng D, Brüschweiler R
Abstract
A robust NMR resonance assignment method...
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[NMR paper] Reliable Resonance Assignments of Selected Residues of Proteins with Known Structure Based on Empirical NMR Chemical Shift Prediction
Reliable Resonance Assignments of Selected Residues of Proteins with Known Structure Based on Empirical NMR Chemical Shift Prediction
Publication date: Available online 7 March 2015
Source:Journal of Magnetic Resonance</br>
Author(s): Da-Wei Li , Dan Meng , Rafael Brüschweiler</br>
A robust NMR resonance assignment method is introduced for proteins whose 3D structure has previously been determined by X-ray crystallography. The goal of the method is to obtain a subset of correct assignments from a parsimonious set of 3D NMR experiments of 15N, 13C labeled proteins....
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[NMR paper] Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations.
Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations.
Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations.
Phys Chem Chem Phys. 2014 Jul 23;
Authors: Zhu T, Zhang JZ, He X
Abstract
In this work, protein side chain (1)H chemical shifts are used as probes to detect and correct side-chain packing errors in protein's NMR structures through structural refinement. By applying the automated...
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07-24-2014 11:56 AM
[NMR paper] An approach to sequential NMR assignments of proteins: application to chemical shift restraint-based structure prediction.
An approach to sequential NMR assignments of proteins: application to chemical shift restraint-based structure prediction.
Related Articles An approach to sequential NMR assignments of proteins: application to chemical shift restraint-based structure prediction.
J Biomol NMR. 2014 Jun 19;
Authors: Wiedemann C, Bellstedt P, Herbst C, Görlach M, Ramachandran R
Abstract
A procedure for the simultaneous acquisition of {HNCOCANH & HCCCONH} chemical shift correlation spectra employing sequential data acquisition for moderately sized...
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06-20-2014 08:14 PM
An approach to sequential NMR assignments of proteins: application to chemical shift restraint-based structure prediction
An approach to sequential NMR assignments of proteins: application to chemical shift restraint-based structure prediction
Abstract
A procedure for the simultaneous acquisition of {HNCOCANH & HCCCONH} chemical shift correlation spectra employing sequential \(^{1}\hbox {H}\) data acquisition for moderately sized proteins is presented. The suitability of the approach for obtaining sequential resonance assignments, including complete ...
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06-19-2014 10:21 PM
[NMR paper] Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.
Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.
Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.
J Biomol NMR. 2013 Apr 28;
Authors: Fritzsching KJ, Yang Y, Schmidt-Rohr K, Hong M
Abstract
We introduce a Python-based program that utilizes the large database of (13)C and (15)N chemical shifts in the Biological Magnetic...
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04-30-2013 10:21 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
[NMR paper] CAMRA: chemical shift based computer aided protein NMR assignments.
CAMRA: chemical shift based computer aided protein NMR assignments.
Related Articles CAMRA: chemical shift based computer aided protein NMR assignments.
J Biomol NMR. 1998 Oct;12(3):395-405
Authors: Gronwald W, Willard L, Jellard T, Boyko RF, Rajarathnam K, Wishart DS, Sönnichsen FD, Sykes BD
A suite of programs called CAMRA (Computer Aided Magnetic Resonance Assignment) has been developed for computer assisted residue-specific assignments of proteins. CAMRA consists of three units: ORB, CAPTURE and PROCESS. ORB predicts NMR chemical shifts...
PPM_One: a static protein structure based chemical shift predictor
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