Share This Author
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…
A smooth particle mesh Ewald method
- U. Essmann, L. Perera, M. Berkowitz, T. Darden, Hsing-Chou Lee, L. Pedersen
- Computer Science
- 15 November 1995
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.
Gene selection for sample classification based on gene expression data: study of sensitivity to choice of parameters of the GA/KNN method
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.
Crystal structure of estrogen sulphotransferase
- Y. Kakuta, L. Pedersen, C. Carter, M. Negishi, L. Pedersen
- BiologyNature Structural Biology
- 1 November 1997
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…
Structure and function of sulfotransferases.
- M. Negishi, L. Pedersen, L. Pedersen
- Chemistry, BiologyArchives of biochemistry and biophysics
- 15 June 2001
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.
Gene assessment and sample classification for gene expression data using a genetic algorithm/k-nearest neighbor method.
- L. Li, T. Darden, C. Weinberg, A. Levine, L. Pedersen
- BiologyCombinatorial chemistry & high throughput…
- 30 November 2001
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).
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…
Conserved structural motifs in the sulfotransferase family.
Role of gamma-carboxyglutamic acid in the calcium-induced structural transition of conantokin G, a conotoxin from the marine snail Conus geographus.
- A. C. Rigby, J. Baleja, L. Li, L. Pedersen, B. Furie, B. Furie
- Chemistry, BiologyBiochemistry
- 16 December 1997
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.
Molecular Insights into DNA Polymerase Deterrents for Ribonucleotide Insertion*♦
- Nisha A. Cavanaugh, W. Beard, V. Batra, L. Perera, L. Pedersen, Samuel H. Wilson
- Biology, ChemistryThe Journal of Biological Chemistry
- 6 July 2011
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.