Browse By Depositor - Professor Alan Mark

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 Browse By Depositor - Professor Alan Mark:
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Schafer, Heiko, Mark, Alan E. and van Gunsteren, Wilfred F. (2000) Absolute entropies from molecular dynamics simulation trajectories. Journal of Chemical Physics, 113 18: 7809-7817. doi:10.1063/1.1309534 221 1 123 Cited 126 times in Scopus126 0
Fioroni, Marco, Burger, Klaus, Mark, Alan E. and Roccatano, Danilo (2000) A new 2,2,2-triflouroethanol model for molecular dynamics simulations. The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces and Biophysical, 104 51: 12347-12354. doi:10.1021/jp002115v 53 17 71 Cited 71 times in Scopus71 0
Malde, AK and Mark, AE (2011) Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexes. Journal of Computer-Aided Molecular Design, 25 1: 1-12. doi:10.1007/s10822-010-9397-6 59   16 Cited 15 times in Scopus15 8
Chen, Rong, Poger, David and Mark, Alan (2011) Effect of high pressure on fully hydrated DPPC and POPC bilayers. The Journal of Physical Chemistry B, 115 5: 1038-1044. doi:10.1021/jp110002q 51 2 11 Cited 12 times in Scopus12 0
Schäfer, Heiko, Van Gunsteren, Wilfred F. and Mark, Alan E. (1999) Estimating relative free energies from a single ensemble: Hydration free energies. Journal of Computational Chemistry, 20 15: 1604-1617. doi:10.1002/(SICI)1096-987X(19991130)20:15<1604::AID-JCC2>3.0.CO;2-A 26 1 49 Cited 49 times in Scopus49 0
Daura, X., van Gunsteren, W. F. and Mark, A. E. (1999) Folding-unfolding thermodynamics of a beta-heptapeptide form equilibrium simulations. Proteins: Structure, Function, and Genetics, 34 3: 269-280. doi:10.1002/(SICI)1097-0134(19990215)34:3 28 1 270 Cited 269 times in Scopus269 0
Marrink, S. J., Tieleman, D. P. and Mark, A. E. (2000) Molecular dynamics simulation of the kinetics of spontaneous micelle formation. Journal of Physical Chemistry B, 104 51: 12165-12173. doi:10.1021/jp001898h 29 1 182 0
Smith, Lorna J., Mark, Alan E., Dobson, Christopher M. and van Gunsteren, Wilfred (1998) Molecular dynamics simulations of peptide fragments from hen lysozyme: Insight into non-native protein conformations. Journal of Molecular Biology, 280 4: 703-719. doi:10.1006/jmbi.1998.1892 29 1 12 Cited 12 times in Scopus12 0
Walser, Regula, Mark, Alan E. and van Gunsteren, Wilfred F. (2000) On the temperature and pressure dependence of a range of properties of a type of water model commonly used in high-temperence protein unfolding simulations. Biophysical Journal, 78 6: 2752-2760. 38 3 28 Cited 28 times in Scopus28
Walser, Regula, Mark, Alan E. and van Gunsteren, Wilfred F. (1999) On the validity of Stokes’ law at the molecular level. Chemical Physics Letters, 303 5-6: 583-586. doi:10.1016/S0009-2614(99)00266-3 31 377 27 Cited 27 times in Scopus27 0
Scott, Walter R. P., Mark, Alan E. and van Gunsteren, W.F. (1998) On using time-averaging restraints in molecular dynamics simulation. Journal of Biomolecular NMR, 12 4: 501-508. doi:10.1023/A:1008306732538 22 1 20 Cited 20 times in Scopus20 0
Daura, Xavier, Mark, Alan E. and van Gunsteren, Wilfred F. (1998) Parametrization of aliphatic CHn united atoms of GROMOS96 force field. Journal of Computational Chemistry, 19 5: 535-547. doi:10.1002/(SICI)1096-987X(19980415)19:5<535::AID-JCC6>3.0.CO;2-N 27 1 242 Cited 241 times in Scopus241 0
Daura, X., van Gunsteren, W. F. and Mark, A. E. (1999) Peptide folding simulations: No solvent required?. Computer Physics Communications, 123 1-3: 97-102. doi:10.1016/S0010-4655(99)00261-1 29 1 30 Cited 29 times in Scopus29 0
Daura, Xavier, Gadermann, Karl, Jaun, Bernhard, Seebach, Dieter, van Gunsteren, Wilfred F. and Mark, Alan E. (1999) Peptide Folding: When simulation meets experiment. Angewandte Chemie, 38 1-2: 236-240. doi:10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M 35 1 491 Cited 487 times in Scopus487 0
Daura, Xavier, Jaun, Bernhard, Seebach, Dieter, van Gunsteren, Wilfred F. and Mark, Alan E. (1998) Reversible peptide folding in solution by molecular dynamics simulation. Journal of Molecular Biology, 280 5: 925-932. doi:10.1006/jmbi.1998.1885 29 1 303 Cited 304 times in Scopus304 0
Walser, Regula, Mark, Alan E., van Gunsteren, Wilfred F., Lauterbach, Monika and Wipff, Georges (2000) The effect of force-field parameters on properties of liquids: Parameterization of a simple three site model for methanol. Journal of Chemical Physics, 112 23: 10450-10459. doi:10.1063/1.481680 41 114 93 Cited 91 times in Scopus91 0
Chen, Rong and Mark, Alan E. (2011) The effect of membrane curvature on the conformation of antimicrobial peptides: Implications for binding and the mechanism of action. European Biophysics Journal, 40 4: 545-553. doi:10.1007/s00249-011-0677-4 50 1 17 Cited 19 times in Scopus19 0
Daura, Xavier, Antes, Iris, van Gunsteren, Wilfred F, Thiel, Walter and Mark, Alan E. (1999) The effect of motional averaging on the calculation of NMR-derived structural properties. Proteins: Structure, Function, and Bioinformatics, 36 4: 542-555. doi:10.1002/(SICI)1097-0134(19990901)36:4<542::AID-PROT17>3.0.CO;2-M 43 17 72 Cited 75 times in Scopus75 0
Bonvin, Alexandre M. J. J., Mark, Alan E. and van Gunsteren, Wilfred F. (2000) The GROMOS96 benchmarks for molecular simulation. Computer Physics Communications, 128 3: 550-557. doi:10.1016/S0010-4655(99)00540-8 28 48 9 Cited 8 times in Scopus8 0
van Gunsteren, Wilfred F. and Mark, Alan E. (1998) Validation of molecular dynamics simulation. Journal of Chemical Physics, 108 15: 6109-6116. doi:10.1063/1.476021 52 202 87 Cited 91 times in Scopus91 0