Jeffery B Klauda

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. ncbi Simulation-based methods for interpreting x-ray data from lipid bilayers
    Jeffery B Klauda
    Laboratory of Computational Biology, National Institutes of Health, Bethesda, Maryland 20892, USA
    Biophys J 90:2796-807. 2006
  2. ncbi Dynamical motions of lipids and a finite size effect in simulations of bilayers
    Jeffery B Klauda
    Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Chem Phys 125:144710. 2006
  3. ncbi Long-range Lennard-Jones and electrostatic interactions in interfaces: application of the isotropic periodic sum method
    Jeffery B Klauda
    Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Phys Chem B 111:4393-400. 2007
  4. ncbi Sugar binding in lactose permease: anomeric state of a disaccharide influences binding structure
    Jeffery B Klauda
    Laboratory of Computational Biology, National Institutes of Health, Bldg 50, 50 South Drive, Bethesda, MD 20892, USA
    J Mol Biol 367:1523-34. 2007
  5. ncbi Rotation of lipids in membranes: molecular dynamics simulation, 31P spin-lattice relaxation, and rigid-body dynamics
    Jeffery B Klauda
    Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Biophys J 94:3074-83. 2008
  6. ncbi Binding and release of cholesterol in the Osh4 protein of yeast
    Rishi P Singh
    Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892 9314, USA
    Proteins 75:468-77. 2009
  7. ncbi An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer
    Jeffery B Klauda
    Laboratory of Biophysical Chemistry, National Institutes of Health, Building 50, 50 South Drive, Bethesda, Maryland 20892, USA
    J Phys Chem B 109:5300-11. 2005
  8. ncbi Collective and noncollective models of NMR relaxation in lipid vesicles and multilayers
    Jeffery B Klauda
    Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Phys Chem B 112:5924-9. 2008
  9. ncbi CHARMMing: a new, flexible web portal for CHARMM
    Benjamin T Miller
    Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Chem Inf Model 48:1920-9. 2008
  10. ncbi Adjacent gauche stabilization in linear alkanes: implications for polymer models and conformational analysis
    Jeffery B Klauda
    J Phys Chem B 109:15684-6. 2005

Collaborators

Detail Information

Publications10

  1. ncbi Simulation-based methods for interpreting x-ray data from lipid bilayers
    Jeffery B Klauda
    Laboratory of Computational Biology, National Institutes of Health, Bethesda, Maryland 20892, USA
    Biophys J 90:2796-807. 2006
    ..This approach is independent of structural models and could be used to determine structural properties of bilayers with different lipids, cholesterol, and peptides...
  2. ncbi Dynamical motions of lipids and a finite size effect in simulations of bilayers
    Jeffery B Klauda
    Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Chem Phys 125:144710. 2006
    ..A third MD simulation of a bilayer with 72 lipids using spherical force-shift electrostatic cutoffs resulted in interdigitated chains, thereby rendering this cutoff method inappropriate...
  3. ncbi Long-range Lennard-Jones and electrostatic interactions in interfaces: application of the isotropic periodic sum method
    Jeffery B Klauda
    Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Phys Chem B 111:4393-400. 2007
    ....
  4. ncbi Sugar binding in lactose permease: anomeric state of a disaccharide influences binding structure
    Jeffery B Klauda
    Laboratory of Computational Biology, National Institutes of Health, Bldg 50, 50 South Drive, Bethesda, MD 20892, USA
    J Mol Biol 367:1523-34. 2007
    ..e. -10.7(+/-0.7) and -3.1(+/-1.0) kcal/mol, respectively. Of the 12 helices in LacY, helix-IV is the least stable with betabeta-(Galp)(2) binding resulting in larger distortion than alphabeta-(Galp)(2)...
  5. ncbi Rotation of lipids in membranes: molecular dynamics simulation, 31P spin-lattice relaxation, and rigid-body dynamics
    Jeffery B Klauda
    Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Biophys J 94:3074-83. 2008
    ....
  6. ncbi Binding and release of cholesterol in the Osh4 protein of yeast
    Rishi P Singh
    Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892 9314, USA
    Proteins 75:468-77. 2009
    ..The mechanism of sterol release is conceptualized as a molecular ladder with the rungs being amino acids or water-mediated amino acids that interact with 3-OH...
  7. ncbi An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer
    Jeffery B Klauda
    Laboratory of Biophysical Chemistry, National Institutes of Health, Building 50, 50 South Drive, Bethesda, Maryland 20892, USA
    J Phys Chem B 109:5300-11. 2005
    ..In addition, C27r simulations of a hydrated DPPC lipid bilayer yield improved agreement with the experimental NMR deuterium order parameters for the aliphatic chain ends...
  8. ncbi Collective and noncollective models of NMR relaxation in lipid vesicles and multilayers
    Jeffery B Klauda
    Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Phys Chem B 112:5924-9. 2008
    ..Modifications to the acyl chain torsional potential energy function used for the simulations substantially improve agreement with experiment...
  9. ncbi CHARMMing: a new, flexible web portal for CHARMM
    Benjamin T Miller
    Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Chem Inf Model 48:1920-9. 2008
    ..Although no software can replace a scientist's own judgment and experience, CHARMMing eases the introduction of newcomers to the molecular modeling discipline by providing a graphical method for running simulations...
  10. ncbi Adjacent gauche stabilization in linear alkanes: implications for polymer models and conformational analysis
    Jeffery B Klauda
    J Phys Chem B 109:15684-6. 2005
    ..This adjacent gauche stabilization should be taken into account when formulating or analyzing rotational isomeric models, carrying out conformational analysis, and developing force fields for alkanes, lipids, and related polymers...