Related ArticlesProtein structure estimation from NMR data by matrix completion.
Eur Biophys J. 2017 Feb 06;:
Authors: Li Z, Li Y, Lei Q, Zhao Q
Abstract
Knowledge of protein structures is very important to understand their corresponding physical and chemical properties. Nuclear Magnetic Resonance (NMR) spectroscopy is one of the main methods to measure protein structure. In this paper, we propose a two-stage approach to calculate the structure of a protein from a highly incomplete distance matrix, where most data are obtained from NMR. We first randomly "guess" a small part of unobservable distances by utilizing the triangle inequality, which is crucial for the second stage. Then we use matrix completion to calculate the protein structure from the obtained incomplete distance matrix. We apply the accelerated proximal gradient algorithm to solve the corresponding optimization problem. Furthermore, the recovery error of our method is analyzed, and its efficiency is demonstrated by several practical examples.
PMID: 28168331 [PubMed - as supplied by publisher]
[NMR paper] NMR Structure of the Myristylated Feline Immunodeficiency Virus Matrix Protein.
NMR Structure of the Myristylated Feline Immunodeficiency Virus Matrix Protein.
Related Articles NMR Structure of the Myristylated Feline Immunodeficiency Virus Matrix Protein.
Viruses. 2015;7(5):2210-2229
Authors: Brown LA, Cox C, Baptiste J, Summers H, Button R, Bahlow K, Spurrier V, Kyser J, Luttge BG, Kuo L, Freed EO, Summers MF
Abstract
Membrane targeting by the Gag proteins of the human immunodeficiency viruses (HIV types-1 and -2) is mediated by Gag's N-terminally myristylated matrix (MA) domain and is dependent on...
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05-06-2015 11:59 AM
Estimation of protein function using template-based alignment of enzyme active ... - 7thSpace Interactive (press release)
Estimation of protein function using template-based alignment of enzyme active ... - 7thSpace Interactive (press release)
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Estimation of protein function using template-based alignment of enzyme active ...
7thSpace Interactive (press release)
261 additional motifs automatically translated from Jonathan Barker's JESS motif set and a set of NMR motifs is under development. Alignments are evaluated by visual superposition, Levenshtein distance and ...
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03-27-2014 03:46 AM
[Question from NMRWiki Q&A forum] VNMRJ Macro - wait until completion of first experiment
VNMRJ Macro - wait until completion of first experiment
I am relatively new to VNMRJ, and am trying to write a macro that executes an array in experiment 1, then, once finished, executes the array in experiment 2, etc. for any pre-determined number of experiments. My first thought was the following:
1) Start experiment n. 2) Use a "repeat" loop querying the status of the current experiment using acqstatus. 3) When acqstatus indicates that experiment n is complete, exit the "repeat" loop and start the next experiment.
The problem that I found is that it was getting stuck in the...
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03-11-2014 11:48 AM
[NMR paper] Peak picking NMR spectral data using non-negative matrix factorization.
Peak picking NMR spectral data using non-negative matrix factorization.
Peak picking NMR spectral data using non-negative matrix factorization.
BMC Bioinformatics. 2014 Feb 11;15(1):46
Authors: Tikole S, Jaravine V, Rogov V, Dötsch V, Güntert P
Abstract
BACKGROUND: Simple peak-picking algorithms, such as those based on lineshape fitting, perform well when peaks are completely resolved in multidimensional NMR spectra, but often produce wrong intensities and frequencies for overlapping peak clusters. For example, NOESY-type spectra...
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02-12-2014 11:48 AM
Bayesian estimation of NMR restraint potential and weight: A validation on a representative set of protein structures.
Bayesian estimation of NMR restraint potential and weight: A validation on a representative set of protein structures.
Bayesian estimation of NMR restraint potential and weight: A validation on a representative set of protein structures.
Proteins. 2011 Jan 6;
Authors: Bernard A, Vranken WF, Bardiaux B, Nilges M, Malliavin TE
The classical procedure for nuclear magnetic resonance structure calculation allocates empirical distance ranges and uses historical values for weighting factors. However, Bayesian analysis suggests that there are more optimal...
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03-03-2011 12:34 PM
[Question from NMRWiki Q&A forum] converting nmrpipe processed data (.ft3 files) to felix matrix
converting nmrpipe processed data (.ft3 files) to felix matrix
I am trying to convert the .ft3 files into a felix matrix using the pipe2mat conversion filter in felix but it doesn't seem to work properly - it does generate a matrix but the size of the matrix is too small and Felix freezes if I try to open it. Does anyone have a script to do so? or maybe you got the felix filter to work?
Check if somebody has answered this question on NMRWiki QA forum
nmrlearner
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12-07-2010 09:54 AM
[NMR paper] Correlation between drug release kinetics from proteineous matrix and matrix structur
Correlation between drug release kinetics from proteineous matrix and matrix structure: EPR and NMR study.
Related Articles Correlation between drug release kinetics from proteineous matrix and matrix structure: EPR and NMR study.
J Pharm Sci. 2000 Mar;89(3):365-81
Authors: Katzhendler I, Mäder K, Friedman M
The present study was conducted in order to probe the microstructure, microviscosity, and hydration properties of matrices containing two model drugs, naproxen sodium (NS) and naproxen (N), and egg albumin (EA) as matrix carrier. The...
Protein structure estimation from NMR data by matrix completion.
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