Related ArticlesFrom Raw Data to Protein Backbone Chemical Shifts Using NMRFx Processing and NMRViewJ Analysis.
Methods Mol Biol. 2018;1688:257-310
Authors: Johnson BA
Abstract
Assignment of the chemical shifts of the backbone atoms (HN, N, CA, CB, and C) of proteins is often a prerequisite to using NMR information in the study of proteins. These chemical shifts and their perturbations are the basis for the analysis of protein dynamics, ligand binding, and backbone conformation. They are generally assigned prior to full side-chain assignments and the determination of the complete three-dimensional molecular structure. This chapter describes the use of two software packages, NMRFx Processor and NMRViewJ, in going from raw NMR data to backbone assignments. The step-by-step procedure describes processing of the data and the use of manual and automated features of the RunAbout tool in NMRViewJ to perform the assignments.
NMRFx Processor: a cross-platform NMR data processing program
NMRFx Processor: a cross-platform NMR data processing program
Abstract
NMRFx Processor is a new program for the processing of NMR data. Written in the Java programming language, NMRFx Processor is a cross-platform application and runs on Linux, Mac OS X and Windows operating systems. The application can be run in both a graphical user interface (GUI) mode and from the command line. Processing scripts are written in the Python programming language and executed so that the low-level Java commands are automatically run in parallel on computers with...
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07-25-2016 04:26 PM
[NMR paper] Application of Data Mining Tools for Classification of Protein Structural Class from Residue Based Averaged NMR Chemical Shifts.
Application of Data Mining Tools for Classification of Protein Structural Class from Residue Based Averaged NMR Chemical Shifts.
Application of Data Mining Tools for Classification of Protein Structural Class from Residue Based Averaged NMR Chemical Shifts.
Biochim Biophys Acta. 2015 Mar 7;
Authors: Kumar AV, Ali RF, Cao Y, Krishnan VV
Abstract
The number of protein sequences deriving from genome sequencing projects is outpacing our knowledge about the function of these proteins. With the gap between experimentally characterized...
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03-12-2015 10:33 AM
Application of Data Mining Tools for Classification of Protein Structural Class from Residue Based Averaged NMR Chemical Shifts
Application of Data Mining Tools for Classification of Protein Structural Class from Residue Based Averaged NMR Chemical Shifts
Publication date: Available online 7 March 2015
Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics</br>
Author(s): Arun.V. Kumar , Rehana F.M. Ali , Yu Cao , V.V. Krishnan</br>
The number of protein sequences deriving from genome sequencing projects is outpacing our knowledge about the function of these proteins. With the gap between experimentally characterized and uncharacterized proteins continuing to widen, it is...
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03-08-2015 01:23 PM
[NMR paper] NMRDSP: An Accurate Prediction of Protein Shape Strings from NMR Chemical Shifts and Sequence Data.
NMRDSP: An Accurate Prediction of Protein Shape Strings from NMR Chemical Shifts and Sequence Data.
Related Articles NMRDSP: An Accurate Prediction of Protein Shape Strings from NMR Chemical Shifts and Sequence Data.
PLoS One. 2013;8(12):e83532
Authors: Mao W, Cong P, Wang Z, Lu L, Zhu Z, Li T
Abstract
Shape string is structural sequence and is an extremely important structure representation of protein backbone conformations. Nuclear magnetic resonance chemical shifts give a strong correlation with the local protein structure, and are...
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01-01-2014 03:05 PM
[NMR paper] Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks.
Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks.
Related Articles Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks.
J Biomol NMR. 2013 Jun 2;
Authors: Shen Y, Bax A
Abstract
A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+....
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06-04-2013 06:31 PM
Local protein backbone folds determined by calculated NMR chemical shifts.
Local protein backbone folds determined by calculated NMR chemical shifts.
Local protein backbone folds determined by calculated NMR chemical shifts.
J Comput Chem. 2011 Sep 9;
Authors: Czajlik A, Hudáky I, Perczel A
Abstract
NMR chemical shifts (CSs: ?N(NH) , ?C(?) , ?C(?) , ?C', ?H(NH) , and ?H(?) ) were computed for the amino acid backbone conformers (?(L) , ?(L) , ?(L) , ?(L) , ?(L) , ?(D) , ?(D) , ?(D) , and ?(D) ) modeled by oligoalanine structures. Topological differences of the extended fold were investigated on single ?-strands,...
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09-10-2011 06:51 PM
[NMR paper] Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its us
Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements.
Related Articles Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements.
J Biomol NMR. 2005 May;32(1):71-81
Authors: Eghbalnia HR, Wang L, Bahrami A, Assadi A, Markley JL
We present an energy model that combines information from the amino acid sequence of a protein and available NMR chemical shifts for the purposes of identifying low...
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11-25-2010 08:21 PM
Analysis of NMR Chemical Shifts in Peptide & Protein Structure Determination-Wang '08
Analysis of NMR Chemical Shifts in Peptide and Protein Structure Determination
By Liya Wang (2008)
Amazon book description
Chemical shifts provide detailed information about non-covalent structure, solvent interactions, ionization constants, ring orientations, hydrogen bond interactions, and other phenomena. Since different chemical shift data sets are not necessarily comparable without corrections or adjustments, the applicability of statistical analysis of NMR chemical shifts to biomolecules has so far been limited. We use the term "congruent" to describe data sets that can be...
From Raw Data to Protein Backbone Chemical Shifts Using NMRFx Processing and NMRViewJ Analysis.
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