Publications Alan Mark
Below is a list of publications from the MD group at the University of Queensland, headed by Professor Alan Mark. Further publications lists can be found at the University of Groningen and ETH Zurich
For reprints email md.secretary@uq.edu.au
Submitted
- Mueller, D.S. and Mark, A.E.
The protonation of histidines in the dengue viral envelope protein triggers irreversible structural changes. Submitted June 2010
- Nair, P.C., Malde, A.K. and Mark, A.E.
Using theory to reconcile experiment: the structural and thermodynamic basis of ligand recognition by Phenylethanolamine N-Methyl Transferase (PNMT). J. Chem. Theory Comput. Submitted December 2010
In press
- (in press)
2011
AM11.01 Malde, A. and Mark, A.E. (2011)
Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexes?
J.Comp. Aided Mol.Des. 25, 1-12
DOI:10.1007/210822-010-9397-6
2010
AM10.01 Poger, D. and Mark, A.E. (2010)
On the Validation of Molecular Dynamics Simulations of Saturated and cis-Monounsaturated phosphatidylcholine Lipid Bilayers: A Comparison with Experiment.
J.Chem.Theory Comput. 6, 325-336.
DOI:10/1021/ct900487a
AM10.02 Poger, D. and Mark, A.E. (2010)
Turning the growth hormone receptor on: Direct evidence that hormone binding induces subunit rotation.
Proteins: Structure, Function, and Bioinformatics. 78, 1163-1174.
DOI:10.1002/prot.22636
AM10.03 Poger, D., van Gunsteren, W.F. and Mark, A.E. (2010)
A New Force Field for Simulating Phosphatidylcholine Bilayers.
J. Comput. Chem. 31, 1117-1125.
DOI:10.1002/jcc.21396
AM10.04 Christ, C.D., Mark, A.E. and van Gunsteren, W.F. (2010)
Basic ingredients of free energy calculations: a review.
J. Comput. Chem. 31, 1569-1582.
DOI:10.1002/jcc.21450
2009
AM09.01 Wassenaar, T., Daura, X., Padrós, E. and Mark, A. E. (2009)
Calcium binding to the Purple Membrane: A Molecular Dynamics study.
Proteins: Structure, Function, and Bioinformatics. 74, 669-681.
DOI:10.1002/prot.22182
AM09.02 Reimers, J. R., McKemmish, L. K., McKenzie, R. H., Mark, A. E. and Hush, N. (2009)
The Weak, Strong, and Coherent Regimes of Fröhlich Condensation and their Applications to Terahertz Medicine and Quantum Consciousness.
Proc. Natl. Acad. Sci. 106, 4219-4224.
DOI:10.1073/pnas.0806273106
AM09.03 Periole, X., Rampioni, A., Vendruscolo, M. and Mark, A. E. (2009)
Factors that affect the degree of twist in b-sheet structures: A molecular dynamics simulation study of a cross- filament of the GNNQQNY peptide.
J. Phys. Chem. B. 113, 1728-1737.
DOI:10.1021/jp8078259
AM09.04 Malde, A. K. and Mark, A. E. (2009)
The Binding and Enantiomeric Selectivity of Threonyl-tRNA Synthetase.
J. Am Chem. Soc. 131, 3848-3849.
DOI:10.1021/ja/9002124
AM09.05 Swiko, M. A., de Vries, A. H., Mark, A. E., Kozubek, A. and Marrink, S. J. (2009)
Disturb or stabilise? A molecular dynamics study of the dual effect of resorcinolic lipids on phospholipid bilayers.
Biophys. J. 96, 3140-3153.
DOI:10.1016/j.bpj.2009.01.040
AM09.06 Periole, X., Allen, L. R., Tamiola, K., Mark, A. E. and Paci, E. (2009)
Probing the free energy landscapes of the FBP28 WW domain by multiple techniques.
J. Comp. Chem. 30, 1059-1068.
DOI:10.1002/jcc.21128
AM09.07 Donnini, S., Villa, A., Groenhof, G., Mark, A. E., Wierenga, R. K. and Juffer, A. H. (2009)
Inclusion of ionization states of ligands in affinity calculations.
Proteins: Structure, Function, and Bioinformatics. 76, 138-150.
DOI:10.1002/prot.22326
AM09.08 Yesylevskyy, S., Marrink, S. J. and Mark, A. E. (2009)
Alternative mechanisms for the interaction of the cell-penetrating peptides Penetratin and the TAT peptide with lipid bilayers.
Biophys. J. 97, 40-49.
DOI:10.1016/j.bpj.2009.03.059
AM09.09 McKemmish, L. K., Reimers, J. R., McKenzie, R. H., Mark, A. E. and Hush, N. S. (2009)
Penrose-Hameroff orchestrated objective-reduction Proposal for human consciousness is not biologically feasible.
Physics Review E. 80, 021912.
DOI:10.1103/PhysRev.E.80.021912
2008
AM08.01 Wassenaar, T.A., Quax, W.J. and Mark, A.E. (2008)
The conformation of the extracellular binding domain of Death Receptor 5 in the presence and absence of the activating ligand TRAIL: A molecular dynamics study.
Proteins, Structure, Function, and Bioinformatics, 70, 333-343.
media:AM_08_01.pdf
AM08.02 Knecht, V., Risselada, H.J., Mark, A.E., and Marrink, S.J. (2008)
Electrophoretic mobility does not always reflect the charge on an oil droplet
Journal of Colloid and Interface Science, 318, 477-486.
media:AM_08_02.pdf
AM08.03 Mueller, D.S., Kampmann, T., Yennamalli, R., Young., P.R., Kobe B., Mark, A.E. (2008)
Histidine protonation and the activation of viral fusion proteins
Biochemical Society Transactions, 36, 43-45
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AM08.04 van Gunsteren. W.F., Dolenc, J., and Mark, A.E. (2008)
Molecular simulation as an aid to experimentalists
Current Opinion in Structural Biology, 18, 149-153
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AM08.05 Cemazar, M., Joshi, A., Daly, N., Mark, A. E. and Craik, D.
The Structure of a two-disulfide intermediate assists in elucidating the oxidative folding pathway of a cyclic cystine knot protein.
Structure 16, 842-851
media:AM_08_05.pdf
AM08.06 Risselada, H.J., Mark, A.E. and Marrink, S.J.
The Application of MFFA Boundary Potentials in MD Simulations of Lipid Vesicles.
J. Phys. Chem. B. 112, 7438-7447
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AM08.07 Zhu, J., Fan, H., Periole, X., Honig, B. and Mark, A. E. (2008)
Refining Homology Models by Combining Replica-Exchange Molecular Dynamics and Statistical Potentials.
Proteins: Structure, Function, and Bioinformatics. 72, 1171-1188.
media:AM_08_07.pdf
AM08.08 Kwan, A. H., Macindoe, I., Vukašin, P. V., Morris, V. K., Kass, I., Gupte, R., Mark, A. E., Templeton, M. D., Mackay, J. P. and Sunde, M. (2008)
The Cys3-Cys4 loop of the hydrophobin EAS is not required for rodlet formation and surface activity.
J. Mol. Biol. 382, 708-720.
media:AM_08_08.pdf
AM08.09 Sengupta, D., Leontiadou, H., Mark, A. E. and Marrink, S. J. (2008)
Toroidal Pores Formed by Antimicrobial Peptides Show Significant Disorder.
Biochim. Biophys. Acta - Biomembranes. 1778, 2308-2317.
media:AM_08_09.pdf
2007
AM07.01 Periole, X. and Mark, A. E. (2007)
Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent
J. Chem. Phys. 126, 014903.
media:AM_07.01.pdf
AM07.02 Chipot, C., Mark, A.E., Pande, V.S. and Simonson, T. (2007)
Applications of Free Energy Calculations to Chemistry and Biology.
In: Free Energy Calculations Theory and Applications in Chemistry and Biology. (Chipot, C.; Pohorille, A. Eds.) Springer. pp. 463-492
AM07.03 Pineiro, A., Banquy, X., Perez-Casas, S., Tovar, E., Garcia, A., Villa, A., Amigo, A., Mark, A.E. and Costas, M. (2007)
On the Characterization of Host-Guest Complexes: Surface Tension, Calorimetry, and Molecular Dynamics of Cyclodextrins with a Non-ionic Surfactant.
J. Phys. Chem. B. 111, 4383-92.
media:AM_07_03.pdf
AM07.04 Leontiadou, H., Mark, A.E. and Marrink, S.J. (2007)
Ion transport across transmembrane pores.
Biophys. J. 92, 12, 4209-15.
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AM07.05 Villa, A., Fan, H., Wassenaar, T.A. and Mark, A. E. (2007)
How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field?
J. Phys. Chem. B. 111, 6015-6025.
media:AM_07_05.pdf
AM07.06 Periole, X., Vendruscolo, M, and Mark, A. E. (2007)
Molecular dynamics simulations from putative transition states of alpha-spectrin SH3 domain.
Proteins, Structure, Function, and Bioinformatics, 69, 536-550.
media:AM_07_06.pdf
2006
AM06.01 Wassenaar, T. A. and Mark, A. E. (2006)
The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions.
J. Comp. Chem. 27, 316-325.
media:AM_06_01.pdf
AM06.02 Villa, A., Mark, A. E., Saracino, G. A. A., Cosentino, U., Pitea, D., Moro, G. and Salmona, M. (2006)
Conformational polymorphism of the PrP106-126 peptide in different environments: A Molecular dynamics study.
J. Phys. Chem. B. 110, 1423-1428.
media:AM_06_02.pdf
AM06.03 Knecht, V., Mark, A. E. and Marrink, S. J. (2006)
Phase behavior of a phospholipid/fatty acid/water mixture studied in atomic detail.
J. Amer. Chem. Soc. 128, 2030-2034.
media:AM_06_03.pdf
AM06.04 Fan, H. and Mark A. E. (2006)
Mimicking the action of GroEL in molecular dynamics simulations: application to the refinement of protein structures.
Protein Sci. 15, 441-8.
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AM06.05 Fan, H., Wang, X. Q., Zhu, J., Robillard, G. T. and Mark, A. E. (2006)
Molecular dynamics simulations of the hydrophobin SC3 at a hydrophobic/hydrophilic interface.
Protens-Structure and Bioinformatics, 64, 863-873.
media:AM_06_05.pdf
AM06.06 Leontiadou, H., Mark, A .E. and Marrink, S.J. (2006)
Antimicrobial peptides in action.
J. Am. Chem. Soc. 128, 12156-12161.
media:AM_06_06.pdf
AM06.07 Kampmann, T., Mueller, D. S., Mark, A. E., Young, P. R. and Kobe, B. (2006)
The role of histidine residues in low-pH-mediated viral membrane fusion.
Structure. 14, 1481-7.
media:AM_06_07.pdf
AM06.08 Siwko, M. E., Marrink, S. J., de Vries, A. H., Kozubek, A., Schoot Uiterkamp, A. J. and Mark A. E. (2006)
Does isoprene protect plant membranes from thermal shock? A molecular dynamics study.
Biochim Biophys Acta. 1768, 198-206.
media:AM_06_08.pdf
2005
AM05.01 Donnini, S., Mark, A. E., Juffer, A. H. and Villa, A. (2005)
Incorporating the effect of ionic strength in free energy calculations using explicit ions.
J. Comp. Chem. 26, 115-122.
media:AM_05_01.pdf
AM05.02 Kovalskyy, D., Dubyna, V., Kanibolotsky, D., Mark, A. E. and Kornelyuk, A. (2005)
A molecular dynamics study of the structural stability of HIV-1 protease under physiological conditions: The role of Na+ions in stabilizing the active site.
Proteins: Structure, Function, and Genetics. 58, 450-458.
media:AM_05_02.pdf
AM05.03 Soto, P., Cladera, J., Mark, A. E. and Daura, X. (2005)
Stability of SIV gp32 fusion peptide single layer protofibrils as monitored by molecular dynamics simulations.
Angew. Chem. Int. Ed. Engl. 17, 1089-1091.
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AM05.04 Knecht, V., Mueller, M., Bonn, M., Marrink, S. J. and Mark, A. E. (2005)
Simulation studies of pore and domain formation in a phospholipid monolayer.
J. Chem. Phys. 122, 024704 1-9.
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AM05.05 Pagel, K., Seeger, K., Seiwert, B., Villa, A., Mark, A. E., Berger, S. and Koksch, B. (2005)
Advanced approaches for the characterization of a de novo designed antiparallel coiled coil peptide.
Org. Biomol. Chem. 3, 1189-1194.
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AM05.06 van den Bosch, M., Swart, M., Snijders, J. G., Berendsen, H.J.C., Mark, A. E., Oostenbrink, C., van Gunsteren, W. F. and Canters, G. W. (2005)
Calculation of the redox potential of the protein azurin and some mutants.
Chembiochem. 6, 738-746.
media:AM_05_06.pdf
AM05.07 de Vries, A. H., Yefimov, S., Mark, A. E. and Marrink, S. J. (2005)
Molecular structure of the lecithin ripple phase.
Proceedings of the National Academy of Sciences of the United States of America. 102, 5392-5396.
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AM05.08 Fan, H., Mark, A. E., Zhu, J. and Honig, B. (2005)
Comparative study of generalized Born models: Protein dynamics.
Proceedings of the National Academy of Sciences of the United States of America. 102, 19, 6760-6764.
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AM05.09 Marrink, S. J., Risselada, J. and Mark, A. E. (2005)
Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model.
Chem. Phys. Lipids. 135, 223-244.
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AM05.10 van der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E. and Berendsen, H. J. C., (2005)
GROMACS: Fast, flexible, and free.
J. Comp. Chem. 26, 1701-1718.
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AM05.11 Pinero, A., Villa, A., Vagt, T., Koksch, B. and Mark, A. E. (2005)
A molecular dynamics study of the formation, stability, and oligomerization state of two designed coiled coils: Possibilities and limitations.
Biophys. J. 89, 3701-3713 2005.
media:AM_05_11.pdf
2004
AM04.01 Fan, H. and Mark, A.E.
Refinement of homology-based protein structures by molecular dynamics simulation techniques
Protein Science 13 (2004) 211-220
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AM04.02 Marrink, S.J., de Vries, A.H. and Mark, A.E.
Coarse Grained model for Semiquantitative Lipid Simulations
J. Phys. Chem. B 108 (2004) 750-760
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AM04.03 de Vries, A.H., Mark, A.E. and Marrink, S.J
The Binary Mixing Behaviour of Phospholipids in a Bilayer: a Molecular Dynamics Study
J. Phys. Chem. B 108 (2004) 2454-2463
media:AM_04_03.pdf
AM04.04 Fan, H. and Mark, A.E
Mimicking the action of folding chaperones in molecular dynamics study: Application to the refinement of Homology Based Protein Structures
Protein Science 13 (2004) 992-999
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AM04.05 Leontiadou, H., Mark, A.E., and Marrink, S.J.
Molecular Dynamics Simulations of Hydrophilic Pores in Lipid Bilayers
Biophys. J. 86 (2004) 2156-2164
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AM04.06 Zangi, R. and Mark, A.E.
Electrofreezing of confined water
J. Chem. Phys. 120 (2004) 7123-7130
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AM04.07 Vries, A.H., Mark, A.E. and Marrink, S.J.
Molecular dynamics simulation of spontaneous formation of a small DPPC vesicle in water in atomistic detail
J. Am. Chem. Sco. 126 (2004) 4488-4489
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AM04.08 Groenhof, G., Bouxin-Cademartory, M., Hess, B., de Visser, S.P., Berendsen, H.J.C., Olivucci, M., Mark, A.E. and Robb, M.A.
Photoactivation of the Photoactive Yellow Protein: Why photo absorbtion triggers a trans-to-cis isomerization of the chromophore in the Protein
J. Am. Chem. Soc. 126 (2004) 4228-4233
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AM04.09 Oostenbrink, C., Villa, A., Mark, A.E. and van Gusnteren, W.F.
A biomolecular force field based on the free enthalpy of hydration and solcation: the GROMOS force-field parameter sets 53A5 and 53A6
J. Comp. Chem. 25 (2004) 1656-1676
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AM04.10 Marrink, S.J. and Mark, A.E.
Molecular view of hexagonal phase formation in phospholipid membranes
Biophys. J. 87 (2004) 3894-3900
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2003
AM03.01 Colombo, G., Marrink, S.J. and Mark, A.E.
Simulation of Mscl Gating in a Bilayer under Stress
Biophys. J. 84 (2003) 2331-2337
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AM03.02 Fioroni, M, Burger, K, Mark, A.E. and Roccatano, D.
The Influence of Trifluoromethyl Groups on the Miscibility of Fluorinated Alcholos with Water: A Molecular Dynamics Simulation Study of 1,1,1-Trifluoro-propan-2-ol in Aqueous Solution
J. Phys. Chem. B 107 (2003) 4855-4861
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AM03.03 Tieleman, D.P., Leontiadou, H., Mark, A.E. and Marrink, S.J.
Simulation of the Pore Formation in Lipid Bilayers by Mechanical Stress and Electric Fields
J. Am. Chem. Soc. 125 (2003) 6382-6383
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AM03.04 Zangi, R. and Mark, A.E.
Monolayer Ice
Phys. Rev. Letters 91 (2003) art. no. 025502
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AM03.05 Zangi, R. and Mark, A.E.
Bilayer ice and alternate liquid phases of confined water
J. Chem. Phys. 119 (2003) 1694-1700
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AM03.06 Fan, H. and Mark, A.E.
Relative Stability of Protein Structures Determined by X-ray Crystallography or NMR Spectroscopy: A Molecular Dynamics Simulation Study
Proteins 53 (2003) 111-120
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AM03.07 Talhout, R., Villa, A., Mark, A.E. and Engberts, J.B.F.N.
Understanding Binding Affinity: A Combined Isothermal Titration Calorimetry/Molecular Dynamics Study of the Binding of a Series of Hydrophobically Modified Benzamidinium Chloride Inhibitors to Trypsin
J. Am. Chem. Soc. 125 (2003) 10570-10579
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AM03.08 Marrink, S.J. and Mark, A.E.
The Mechanism of Vesicle Fusion as Revealed by Molecular Dynamics Simulations
J. Am. Chem. Soc. 125 (2003) 11144-11145
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AM03.09 Marrink, S.J. and Mark, A.E.
Molecular Dynamics Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles
J. Am. Chem. Soc. 125 (2003) 15233-15242
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AM03.10 Villa, A., Zangi, R., Pieffert, G. and Mark, A.E.
Sampling and convergence in free energy calculations of protein-ligand interactions: The binding of triphenoxypyridine derivatives to Factor Xa and Trypsin
J. Comp. Aided Mol. Des. 17 (2003) 673-686
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2002
AM02.01 Villa, A. and Mark, A.E.
Calculation of the Free Energy of Solvation for Neutral Analogues of Amino Acid Side Chains
J. Comp. Chem. 23 (2002) 548-553
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AM02.02 Schäfer, H., Smith, L.J., Mark, A.E. and van Gunsteren, W.F.
Entropy Calculations of the Molten Globule State of a Protein: Side-Chain Entropies of alpha-Lactalbumin
Proteins 46 (2002) 215-224
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AM02.03 Colombo, G., Roccatano, D. and Mark, A.E.
Folding and Stability of the Three-Stranded beta-Sheet Peptide Betnova: Insights for Molecular Dynamics Simulations
Proteins 26 (2002) 380-392
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AM02.04 Marrink, S.J and Mark, A.E.
Molecular Dynamics Simulations of Mixed Micelles Modeling Human Bile
Biochemistry 41 (2002) 5375-5382
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AM02.05 Groenhof, G., Lensink, M.F., Berendsen, H.J.C., Snijders, J.G. and Mark, A.E.
Signal Transduction in the Photoactive Yellow Protein. I: Photon Absorption and the Isomerization of the Chromophore
Proteins 48 (2002) 202-211
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AM02.06 Groenhof, G., Lensink, M.F., Berendsen, H.J.C., Mark, A.E. and Hoffman, A.C.
Signal Transduction in the Photoactive Yellow Protein. II: Proton Transfer Initiates Conformational Changes
Proteins 48 (2002) 212-219
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AM02.07 Zangi, R., de Vocht, M.L, Robillard, G.T. and Mark, A.E.
Molecular Dynamics Study of the Folding of Hydrophobin SC3 at a Hydrophilic/Hydrophobic Interface
Biophys. J. 83 (2002) 112-124
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AM02.08 Feenstra, K. A., Peter, C., Scheek, R.M., van Gunsteren, W.F. and Mark, A.E.
A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities) in small peptides
J. Biomol. NMR 23 (2002) 181-194
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AM02.09 van der Berg, P.A.W., Feenstra, K.A., Mark, A.E., Berendsen, H.J.C. and Visser, A.J.W.G.
Dynamic Conformations of Flavin Adenine Dinucleotide: Simulated Molecular Dynamics of the Flavin Cofactor related to the Time-Resolved Fluorescence Characteristics
J. Phys. Chem. B 106 (2002) 8858-8869
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AM02.10 Apol, M.E.F., Berendsen, H.J.C., Mark, A.E. and Hoffman, A.C.
Interparticle Forces for DEM by MD Simulations
Proceed. 4th World Cong. on Particle Tech. Sydney (2002)
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AM02.11 Roccatano, D., Colombo, G. Fioroni, M. and Mark, A.E.
Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary structure formation in peptides: A molecular dynamics study
Proc. Natl. Acad. Sci. 99 (2002) 12179-12184
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AM02.12 van Gunsteren, W.F., Daura, X. and Mark, A.E.
Computation of free energy
Helv. Chim. Acta 85 (2002) 3113-3129
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AM02.13 Soto, P. and Mark, A.E.
The effect of the neglect of electronic polarization in peptide folding simulations
J. Phys. Chem. B 106 (2002) 12830-12833
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2001
AM01.01 Bürgi, R., Daura, X., Mark, A., Belaanda, M., Mammi, S., Peffion, E., and van Gunsteren, W.F.
Folding study of an Aib-rich peptide in DMSO by moelcuar dynamics simulations
J. Peptide Res. 57 (2001) 107-118
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AM01.02 Walser, R., Hess, B., Mark, A.E. and van Gunsteren, W.F.
Further investigation on the validity of the Strokes-Einstein behaviour at the molecular level
Chem. Phys. Letters 334 (2001) 337-342
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AM01.03 Zangi, R., Kovacs, H., van Gunsteren, W.F., Johansson, J. and Mark, A.E.
Free Energy Barrier Estimation of Unfolding the alpha-Helical Surfactant-Associated Polypeptide C
Proteins 43 (2001) 395-402
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AM01.04 Schäfer, H., Daura, X., Mark, A.E. and van Gunsteren, W.F.
Entropy Calculations on a Reversibly Folding Peptide: Changes in Solute Free Energy Cannot Explain Folding Behaviour
Proteins 43 (2001) 45-56
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AM01.05 de Groot, B.L., Daura, X., Mark, A.E. and Grubmüller, H.
Essential dynamics of reversible peptide folding: Memory-free conformational dynamics governed by internal hydrogen bonds
J. Mol. Biol. 309 (2001) 299-313
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AM01.06 Roccatano, D., Mark, A.E. and Hayward, S.
Investigation of the mechanism of domain closure in citrate synthase by molecular dynamics simulation
J. Mol. Biol. 310 (2001) 1039-1053
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AM01.07 Marrink, S.J., Lindahl, E., Edholm, O. and Mark, A.E.
Simulation of the spontaneous aggregation of phospholipids into bilayers
J. Am. Chem. Soc. 123 (2001) 8638-8639
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AM01.08 Fioroni, M., Burger, K, Mark, A.E. and Roccatano, D.
Model of 1,1,1,3,3,3-hexafluoro-propan-2-ol for Molecular Dynamics Simulations
J. Phys. Chem. B 105 (2001) 10967-10975
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AM01.09 Marrink, S.J. and Mark, A.E.
Effect of Undulations on the Surface Tension in Simulate Bilayers
J. Phys. Chem. B 105 (2001) 6122-6127
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2000
AM00.01 Walser, R., Mark, A.E., van Gunsteren, W.F., Lauterbach, M. and Wipff, G.
The effect of force-field parameters on properties of liquids: Parameterization of a simple three site model for methanol.
J. Chem. Phys. 112 (2000) 10450-10459
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AM00.02 Bonvin, A.M.J.J., Mark, A.E. and van Gunsteren, W.F.
The GROMOS96 Benchmarks for Molecular Simulation
Comput. Phys. Commun. 128 (2000) 550-557
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AM00.03 Walser, R., Mark, A.E. and van Gunsteren, W.F.
On the Temperature and Pressure Dependence of a Range of Properties of a Type of Water Model Commonly Used in High-Temperature Protein
Unfolding Simulations
Biophys. J. 78 (2000) 2752-2760
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AM00.04 Marrink, S.J., Tieleman, D.P and Mark, A.E.
Molecular Dynamics Simulation of the Kinetics of Spontaneous Micelle Formation
J. Phys. Chem. B 104 (2000) 12165-12173
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AM00.05 Fioroni, M., Burger, K., Mark, A.E. and Roccatano, D.
A New 2,2,2-Trifluoroethanol Model for Molecular Dynamics Simulations
J. Phys. Chem. B 104 (2000) 12347-12354
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AM00.06 Schäfer H., Mark, A.E. and van Gunsteren, W.F.
Absolute entropies from molecular dynamics simulation trajectories
J. Chem. Phys. 113 (2000) 7809-7817
media:AM_00_06.pdf
1999
AM99.01 Mark, A.E., Schäferm H., Liu, H. and van Gunsteren, W.F.
Estimating relative free energies from a single simulation of an initial state
In: “Computational Molecular Dynamics: Challenges, Methods, Ideas”, Proceedings of the 2nd Intl. Symp. on Algorithms for Macromol. Mod.
P. Deuflhard, J. Hermans, B. Leimkuhler, A.E. Mark, S. Reich, R.D. Skeel eds., Springe-Verlag, Berlin (1999) 149-162
AM99.02 Daura, X., Gadermann, K., Jaun, B., Seebach, D., van Gunsteren, W.F. and Mark, A.E.
Peptide Folding: When simulation meets experiment
Angew. Chemie Intl. Ed. 38 (1999) 236-240
media:AM_99_02.pdf
AM99.03 Daura, X., van Gunsteren, W.F. and Mark, A.E.
Folding-unfolding thermodynamics of a beta-heptapeptide form equilibrium simulations
Proteins 34 (1999) 269-280
media:AM_99_03.pdf
AM99.04 Walser, R., Mark, A.E. and van Gunsteren, W.F.
On the validity of Stokes’ law at the molecular level
Chem. Phys. Letters 303 (1999) 583-586
media:AM_99_04.pdf
AM99.05 Scott, W.R.P., Hühenberger, P.H., Tironi, I.G., Mark, A.E., Billeter, S.R., Fenner, J., Torda, A.E., Huber, T., Krüger, P. and van Gunsteren, W.F.
The GROMOS Biomolecular Simulation Program Package
J. Phys. Chem. A 103 (1999) 3596-3607
media:AM_99_05.pdf
AM99.06 Daura, X., van Gunsteren, W.F. and Mark, A.E.
Peptide folding simulations: No solvent required?
Comput. Phys. Commun. 123 (1999) 97-102
media:AM_99_06.pdf
AM99.07 Schäfer, H., van Gunsteren, W.F. and Mark, A.E.
Estimating Relative Free Energies from a Single Ensemble: Hydration Free Energies
J. Comput. Chem. 20 (1999) 1604-1617
media:AM_99_07.pdf
AM99.08 Daura, X. Antes, I., van Gunsteren, W.F., Thiel, W. and Mark, A.E.
The Effect of Motional Averaging on the Calculation of NMR-Derived Structural Properties
Proteins 36 (1999) 542-555
media:AM_99_08.pdf
1998
AM98.01 Daura, X., Mark, A.E., and van Gunsteren, W.F.
Parameterization of Aliphatic CHn united atoms of the GROMOS96 force field
J. Comp. Chem. 19 (1998) 535-547
media:AM_98_01.pdf
AM98.02 Smith, L.J, Mark, A.E., Dobson, C.M. and van Gunsteren, W.F.
Molecular dynamics simulations of peptide fragments from hen lysozyme: Insight into non-native protein conformations
J. Mol. Biol. 280 (1998) 703-719
media:AM_98_02.pdf
AM98.03 van Gunsteren, W.F. and Mark, A.E.
Validation of molecular dynamics simulation
J. Chem. Phys. 108 (1998) 6109-6116
media:AM_98_03.pdf
AM98.04 Daura, X., Jaun, B., Seebahk, D., van Gunsteren, W.F. and Mark, A.E.
Reversible peptide folding in solution by molecular dynamics simulation
J. Mol. Biol. 280 (1998) 925-932
media:AM_98_04.pdf
AM98.05 van Gunsteren, W.F., Daura, X. and Mark, A.E.
The GROMOS force field
In: Encyclopaedia of Computational Chemistry 2 P. von Rague Schleyer ed., John Wiley & Sons (1998) 1211-1216
AM98.06 Scott, W.R.P., Mark, A.E. and van Gunsteren, W.F.
On using time-averaging restraints in molecular dynamics simulation.
J. Biomol. NMR 12 (1998) 501-508
media:AM_98_06.pdf
AM98.07 Mark, A.E.
Free energy perturbation calculations
In: Encyclopaedia of Computational Chemistry 2 P. von Rague Schleyer ed., John Wiley & Sons (1998) 1070-1083
media:AM_98_07.pdf
1997
AM97.01 Kovacs, H., Mark, A.E., and van Gunsteren, W.F.
Solvent Structure at a hydrophobic surface
Proteins 27 (1996) 395-404
media:AM_97_01.pdf
AM97.02 Lauterbach, M., Wipff, G., Mark, A.E., and van Gunsteren, W.F.
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 (1991) 699-708
1996
AM96.01 Liu, H., Mark, A.E., and van Gunsteren, W.F.
Estimating the Relative Free Energy of Differen Molecular States with Respect to a Single Reference State
J. Phys. Chem. 100 (1996) 9485-9494
media:AM_96_01.pdf
AM96.02 Daura, X., Hühenberger, P.H., Mark, A.E., Querol, E., Avilés, F.X. and van Gunsteren, W.F.
Free Energies of Transfer Trp Analogs from Chloroform to Water: Comparison of Theory and Experiment and the Importance of Adequate Treatment of Electrostatic and Internal Interactions
J. Am. Chem. Soc. 118 (1996) 6285-6294
media:AM_96_02.pdf
AM96.03 van Gunsteren, W.F., Billeter, S.R., Eising, A.A., Hühenberger, P.H., Krüger, P.K. H.C., Mark, A.E., Scott, W.R.P., and Tironi, I.G.
Biomolecular Simulation: The GROMOS96 Manual and User Guide(1996)
vdf Hoschulverlag AG, Zürich.
1995
AM95.01 Mark, A.E. and van Gunsteren, W.F.
Free Energy Calculations in Drug Design: A Practical Guide
In: “New Perspectives in Drug Design” Proceedings of the 9th Intl. Rhoune-Poulenc Rorer Roundtable 11-13 April, 1994, Turnberry, Scotland, P.M. Dean, G. Jolles, C.G. Newton eds., Academic Press Ltd., (1995) 185-200
AM95.02 Hühenberger, P.H., Mark, A.E. and van Gunsteren, W.F.
Computational Approaches to Study Protein Unfolding: Hen Egg White Lysozyme as a Case Study
Proteins 21 (1995) 196-213
media:AM_95_02.pdf
AM95.03Kovacs, H., Mark, A.E., Johansson, J. and van Gunsteren, W.F.
The Effect of Environment on the Stability of an Integral Membrane Helix: Molecular Dynamics Simulations of Surfactant Protein C in Chloroform, Methanol and Water
J. Mol. Biol. 247 (1995) 808 -822
media:AM_95_03.pdf
AM95.04 van Gunsteren, W.F., Hühenberger, P.H., Kovacs, H., Mark, A.E., and Schiffer, C.A.
Investigation of the protein unfolding and stability by computer simulation
Phi. Trans. R. Soc. Lond. B. Biol. Sci. 348 (1995) 49-59
media:AM_95_04.pdf
AM95.05 Hühenberger, P.H., Mark, A.E., and van Gunsteren, W.F.
Fluctuation and Cross-correlation Analysis of Protein Motions Observed in Nanosecond Molecular Dynamics Simulations
J. Mol. Biol. 252 (1995) 492-503
media:AM_95_05.pdf
AM95.06 Smith, L.J., Mark, A.E., Dobson, C.M. and van Gunsteren, W.F.
Comparison of MD Simulations and NMR Experiments for Hen Lysozyme: Analysis of Local Fluctuations, Cooperative Motions and Global Changes
Biochemistry 34 (1995) 10918-10931
media:AM_95_06.pdf
AM95.07 van Gunsteren, W.F., Hühenberger, P.H., Mark, A.E., Smith, P.E. and Tironi, I. G.
Computer simulation of protein motion
Computer Phys. Communications 91 (1995) 305-319
media:AM_95_07.pdf
AM95.08 Mark, A.E., Xu, Y., Liu, H., and van Gunsteren, W.F.
Rapid non-empirical approaches for estimating relative binding free energies
Acta Biochim. Polonica 45 (1995) 525-536
1994
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1992
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1991
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1990
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1988
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1986
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1984
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