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1998 Journal Article Molecular dynamics simulations of peptide fragments from hen lysozyme: Insight into non-native protein conformationsSmith, 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 |
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1998 Journal Article Parametrization of aliphatic CHn united atoms of GROMOS96 force fieldDaura, 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)19:53.0.CO;2-N |
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1998 Journal Article Validation of molecular dynamics simulationvan 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 |
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1998 Book Chapter Free energy perturbation calculationsMark, Alan E. (1998). Free energy perturbation calculations. Encyclopedia of Computational Chemistry. edited by Paul von Ragué Schleyer. Chichester, United Kingdom: John Wiley & Sons. doi: 10.1002/0470845015.cfa010 |
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1997 Journal Article Liquid-liquid ion extraction: Influence of the water content of the organic phase on the ion extraction selectivity. An MD and FEP study of calix[4]crown-6 alkali cation complexes in binary chloroform-water mixturesLauterbach, M, Wipff, G, Mark, A and van Gunsteren, WF (1997). Liquid-liquid ion extraction: Influence of the water content of the organic phase on the ion extraction selectivity. An MD and FEP study of calix[4]crown-6 alkali cation complexes in binary chloroform-water mixtures. Gazzetta Chimica Italiana, 127 (11), 699-708. |
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1997 Journal Article Solvent structure at a hydrophobic protein surfaceKovacs, H, Mark, AE and vanGunsteren, WF (1997). Solvent structure at a hydrophobic protein surface. Proteins-Structure Function and Genetics, 27 (3), 395-404. doi: 10.1002/(SICI)1097-0134(199703)27:33.0.CO;2-C |
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1996 Journal Article Free energies of transfer of Trp analogs from chloroform to water: Comparison of theory and experiment and the importance of adequate treatment of electrostatic and internal interactionsDaura, X, Hunenberger, PH, Mark, AE, Querol, E, Aviles, FX and vanGunsteren, WF (1996). Free energies of transfer of Trp analogs from chloroform to water: Comparison of theory and experiment and the importance of adequate treatment of electrostatic and internal interactions. Journal of the American Chemical Society, 118 (26), 6285-6294. doi: 10.1021/ja9537944 |
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1996 Journal Article Estimating the relative free energy of different molecular states with respect to a single reference stateLiu, HY, Mark, AE and vanGunsteren, WF (1996). Estimating the relative free energy of different molecular states with respect to a single reference state. Journal of Physical Chemistry, 100 (22), 9485-9494. doi: 10.1021/jp9605212 |
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1995 Journal Article Computer simulation of protein motionVangunsteren, WF, Hunenberger, PH, Mark, AE, Smith, PE and Tironi, IG (1995). Computer simulation of protein motion. Computer Physics Communications, 91 (1-3), 305-319. doi: 10.1016/0010-4655(95)00055-K |
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1995 Journal Article Comparison of Md Simulations and Nmr Experiments for Hen Lysozyme - Analysis of Local Fluctuations, Cooperative Motions, and Global ChangesSmith, LJ, Mark, AE, Dobson, CM and Vangunsteren, WF (1995). Comparison of Md Simulations and Nmr Experiments for Hen Lysozyme - Analysis of Local Fluctuations, Cooperative Motions, and Global Changes. Biochemistry, 34 (34), 10918-10931. doi: 10.1021/bi00034a026 |
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1995 Journal Article The effect of environment on the stability of an integral membrane helix: molecular dynamics simulations of surfactant protein C in chloroform, methanol and waterKovacs, Helena, Mark, Alan E., Johansson, Jan and Vangunsteren, Wilfred F. van (1995). The effect of environment on the stability of an integral membrane helix: molecular dynamics simulations of surfactant protein C in chloroform, methanol and water. Journal of Molecular Biology, 247 (4), 808-822. doi: 10.1016/S0022-2836(05)80156-1 |
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1995 Journal Article Investigation of Protein Unfolding and Stability by Computer-SimulationVangunsteren, WF, Hunenberger, PH, Kovacs, H, Mark, AE and Schiffer, CA (1995). Investigation of Protein Unfolding and Stability by Computer-Simulation. Philosophical Transactions of the Royal Society of London Series B-Biological Sciences, 348 (1323), 49-59. doi: 10.1098/rstb.1995.0045 |
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1995 Conference Publication Free energy calculations in drug design: A practical guideMark, AE and Vangunsteren, WF (1995). Free energy calculations in drug design: A practical guide. 9th International Round Table of the Rhone-Poulenc-Rorer-Foundation on New Perspectives in Drug Design, Turnberry Scotland, Apr, 1994. LONDON: ACADEMIC PRESS LTD. |
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1995 Journal Article Rapid non-empirical approaches for estimating relative binding free energiesMark, AE, Xu, YW, Liu, HY and vanGunsteren, WF (1995). Rapid non-empirical approaches for estimating relative binding free energies. Acta Biochimica Polonica, 42 (4), 525-535. |
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1995 Journal Article Computational approaches to study protein unfolding: Hen egg white lysozyme as a case studyHunenberger, PH, Mark, AE and Vangunsteren, WF (1995). Computational approaches to study protein unfolding: Hen egg white lysozyme as a case study. Proteins: Structure, Function and Genetics, 21 (3), 196-213. doi: 10.1002/prot.340210303 |
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1995 Journal Article Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulationsHunenberger, PH, Mark, AE and Vangunsteren, WF (1995). Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations. Journal of Molecular Biology, 252 (4), 492-503. doi: 10.1006/jmbi.1995.0514 |
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1994 Journal Article Fundamentals of Drug Design From a Biophysical ViewpointVangunsteren, WF, King, PM and Mark, AE (1994). Fundamentals of Drug Design From a Biophysical Viewpoint. Quarterly Reviews of Biophysics, 27 (4), 435-481. doi: 10.1017/S0033583500003103 |
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1994 Journal Article Decomposition of the Free-Energy of a System in Terms of Specific Interactions - Implications for Theoretical and Experimental StudiesMark, AE and Vangunsteren, WF (1994). Decomposition of the Free-Energy of a System in Terms of Specific Interactions - Implications for Theoretical and Experimental Studies. Journal of Molecular Biology, 240 (2), 167-176. doi: 10.1006/jmbi.1994.1430 |
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1994 Journal Article Convergence Properties of Free-Energy Calculations - Alpha-Cyclodextrin Complexes as a Case-StudyMark, AE, Vanhelden, SP, Smith, PE, Janssen, Lhm and Vangunsteren, WF (1994). Convergence Properties of Free-Energy Calculations - Alpha-Cyclodextrin Complexes as a Case-Study. Journal of the American Chemical Society, 116 (14), 6293-6302. doi: 10.1021/ja00093a032 |
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1994 Journal Article Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulationsBeutler, TC, Mark, AE, Vanschaik, RC, Gerber, PR and Vangunsteren, WF (1994). Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations. Chemical Physics Letters, 222 (6), 529-539. doi: 10.1016/0009-2614(94)00397-1 |
