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Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems
An N⋅log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented. The method is based on interpolation of the reciprocal space Ewald sums and evaluation of…
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A smooth particle mesh Ewald method
TLDR
It is demonstrated that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N), which is comparable to that of a simple truncation method of 10 A or less.
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Gene selection for sample classification based on gene expression data: study of sensitivity to choice of parameters of the GA/KNN method
TLDR
The GA/KNN method is capable of selecting a subset of predictive genes from a large noisy data set for sample classification and is a multivariate approach that can capture the correlated structure in the data.
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Crystal structure of estrogen sulphotransferase
The structure of estrogen sulphotransferase has been solved in the presence of inactive cofactor PAP and substrate 17β-estradiol. This structure reveals structural similarities between cytosolic…
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Structure and function of sulfotransferases.
TLDR
Structural analysis of the PAPS-, PAP-, substrate-, and/or orthovanadate (VO(3-)(4))-bound enzymes has revealed the common molecular mechanism of the transfer reaction catalyzed by sulfotransferses, and opened a new era for the study of sulfotranferases.
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Gene assessment and sample classification for gene expression data using a genetic algorithm/k-nearest neighbor method.
TLDR
This approach combines a genetic algorithm (GA) and the k-nearest neighbor (KNN) method to identify genes that jointly can discriminate between two types of samples (e.g. normal vs. tumor).
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The effect of long‐range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods
Simulations of the HIV‐1 protease unit cell using a 9 A cutoff, 9/18 A ‘‘twin‐range’’ cutoff, and full Ewald sums have been carried out to 300 ps. The results indicate that long‐range electrostatic…
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Conserved structural motifs in the sulfotransferase family.
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Role of gamma-carboxyglutamic acid in the calcium-induced structural transition of conantokin G, a conotoxin from the marine snail Conus geographus.
TLDR
The three-dimensional structure of the conantokin G/Ca2+ complex is determined by two-dimensional 1H NMR spectroscopy and compared to the high-resolution structure of conantkin G in the absence of metal ions.
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Molecular Insights into DNA Polymerase Deterrents for Ribonucleotide Insertion*♦
TLDR
The results support a model where DNA polymerase β utilizes two strategies, steric and geometric, with a single protein residue to deter ribonucleotide insertion, and suggest that rCTP is well accommodated in the active site but that O2′ of r CTP and the carbonyl oxygen of Tyr-271 or Ala-271 are unusually close.
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