Skip to ContentSkip to Navigation
OnderzoekZernike (ZIAM)

Refereed academic publications of 1998

Molecular Dynamics
  1. Amadei, A., Apol, M.E.F. & Berendsen, H.J.C. On the use of the quasi-Gaussian entropy theory in noncanonical ensembles. I. Prediction of temperature dependence of thermodynamic properties. Journal of Chemical Physics 109 (8) 3004-3016 (1998)

  2. Apol, M.E.F., Amadei, A. & Berendsen, H.J.C. On the use of the quasi-Gaussian entropy theory in noncanonical ensembles. II. Prediction of density dependence of thermodynamic properties. Journal of Chemical Physics 109 (8) 3017-3027 (1998)

  3. Berendsen, H.J.C. Protein folding - A glimpse of the holy grail? Science 282 (5389) 642-643 (1998)

  4. Creveld, L.D., Amadei, A., van Schaik, R.C., Pepermans, H.A.M., de Vlieg, J. & Berendsen, H.J.C. Identification of functional and unfolding motions of cutinase as obtained from molecular dynamics computer simulations. Proteins-Structure Function and Genetics 33 (2) 253-264 (1998)

  5. Daura, X., Mark, A.E. & Gunsteren, W.F.v. Parametrization of aliphatic CHn united atoms of GROMOS96 force field. Journal of Computational Chemistry 19 (5) 535-547 (1998)

  6. Daura, X., Jaun, B., Seebach, D., Gunsteren, W.F.v. & Mark, A.E. Reversible peptide folding in solution by molecular dynamics simulation. Journal of Molecular Biology 280 (5) 925-932 (1998)

  7. de Groot, B.L., Hayward, S., van Aalten, D.M.F., Amadei, A. & Berendsen, H.J.C. Domain motions in bacteriophage T4 lysozyme: A comparison between molecular dynamics and crystallographic data. Proteins-Structure Function and Genetics 31 (2) 116-127 (1998)

  8. Groenhof, G., Lensink, M.F. & Berendsen, H.J.C. Exploring the photoactive yellow protein photocycle by combining quantum mechanics and molecular dynamics. Journal of Molecular Graphics & Modelling 16 (4-6) 277 (1998)

  9. Gunsteren, W.F.v. & Mark, A.E. Validation of molecular dynamics simulation. Journal of Chemical Physics 108 (15) 6109-6116 (1998)

  10. Hayward, S. & Berendsen, H.J.C. Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme. Proteins-Structure Function and Genetics 30 (2) 144-154 (1998)

  11. Langedijk, J.P.M., de Groot, B.L., Berendsen, H.J.C. & van Oirschot, J.T. Structural homology of the central conserved region of the attachment protein G of respiratory syncytial virus with the fourth subdomain of 55-kDa tumor necrosis factor receptor. Virology 243 (2) 293-302 (1998)

  12. Lensink, M.F., Mavri, J. & Berendsen, H.J.C. Simulation of a slow reaction with quantum character-neutral hydrolysis of a carboxylic ester. Journal of Molecular Graphics & Modelling 16 (4-6) 278 (1998)

  13. Maurits, N.M., Zvelindovsky, A.V.M. & Fraaije, J.G.E.M. Equation of state and stress tensor in inhomogeneous compressible copolymer melts: Dynamic mean-field density functional approach. Journal of Chemical Physics 108 (6) 2638-2650 (1998)

  14. Maurits, N.M., Zvelindovsky, A.V.M., Sevink, G.J.A., van Vlimmeren, B.A.C. & Fraaije, J.G.E.M. Hydrodynamic effects in three-dimensional microphase separation of block copolymers: Dynamic mean-field density functional approach. Journal of Chemical Physics 108 (21) 9150-9154 (1998)

  15. Roccatano, D., Amadei, A., Apol, M.E.F., Di Nola, A. & Berendsen, H.J.C. Application of the quasi-Gaussian entropy theory to molecular dynamics simulations of Lennard-Jones fluids. Journal of Chemical Physics 109 (15) 6358-6363 (1998)

  16. Roccatano, D., Berendsen, H.J.C. & D'Angelo, P. Assessment of the validity of intermolecular potential models used in molecular dynamics simulations by extended x-ray absorption fine structure spectroscopy: A case study of Sr2+ in methanol solution. Journal of Chemical Physics 108 (22) 9487-9497 (1998)

  17. Sansom, M.S.P., Breed, J., Berendsen, H.J.C. & Tieleman, P. Alamethicin channels - Simulation studies. Biophysical Journal 74 (2) A232 (1998)

  18. Sansom, M.S.P., Tieleman, D.P., Forrest, L.R. & Berendsen, H.J.C. Molecular dynamics simulations of membranes with embedded proteins and peptides: porin, alamethicin and influenza virus M2. Biochemical Society Transactions 26 (3) 438-443 (1998)

  19. Scott, W.R.P., Mark, A.E. & Gunsteren, W.F.v. On using time-averaging restraints in molecular dynamics simulation. Journal of Biomolecular Nmr 12 (4) 501-508 (1998)

  20. Smith, L.J., Mark, A.E., Dobson, C.M. & Gunsteren, W.F.v. Molecular dynamics simulations of peptide fragments from hen lysozyme: Insight into non-native protein conformations. Journal of Molecular Biology 280 (4) 703-719 (1998)

  21. Tieleman, D.P. & Berendsen, H.J.C. A molecular dynamics study of the pores formed by E-coli OmpF porin in a fully hydrated pope bilayer. Biophysical Journal 74 (2) A392 (1998)

  22. Tieleman, D.P. & Berendsen, H.J.C. A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer. Biophysical Journal 74 (6) 2786-2801 (1998)

  23. Tieleman, D.P., Breed, J., Berendsen, H.J.C. & Sansom, M.S.P. Alamethicin channels in a membrane: molecular dynamics simulations. Faraday Discussions (111) 209-223 (1998)

  24. Tieleman, D.P., Forrest, L.R., Sansom, M.S.P. & Berendsen, H.J.C. Lipid properties and the orientation of aromatic residues in OmpF, influenza M2, and alamethicin systems: Molecular dynamics simulations. Biochemistry 37 (50) 17554-17561 (1998)

  25. van der Spoel, D., van Maaren, P.J. & Berendsen, H.J.C. A systematic study of water models for molecular simulation: Derivation of water models optimized for use with a reaction field. Journal of Chemical Physics 108 (24) 10220-10230 (1998)

  26. Veltman, O.R., Vriend, G., Berendsen, H.J.C., van den Burg, B., Venema, G. & Eijsink, V.G.H. A single calcium binding site is crucial for the calcium- dependent thermal stability of thermolysin-like proteases. Biochemistry 37 (15) 5312-5319 (1998)

  27. Vriend, G., Berendsen, H.J.C., van den Burg, B., Venema, G. & Eijsink, V.G.H. Early steps in the unfolding of thermolysin-like proteases. Journal of Biological Chemistry 273 (52) 35074-35077 (1998)

  28. Zvelindovsky, A.V.M., Sevink, G.J.A., van Vlimmeren, B.A.C., Maurits, N.M. & Fraaije, J.G.E.M. Three-dimensional mesoscale dynamics of block copolymers under shear: The dynamic density-functional approach. Physical Review E 57 (5) R4879-R4882 (1998)

  29. Zvelindovsky, A.V.M., van Vlimmeren, B.A.C., Sevink, G.J.A., Maurits, N.M. & Fraaije, J.G.E.M. Three-dimensional simulation of hexagonal phase of a specific polymer system under shear: The dynamic density functional approach. Journal of Chemical Physics 109 (20) 8751-8754 (1998)

Laatst gewijzigd:22 oktober 2012 14:29