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

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/s10822-010-9397-6

AM11.02 Xue, Y., O'Mara, M., Surawski, P., Trau, M. and Mark, A.E. (2011)
The effect of polyethylene glycol (PEG) spacers on the conformational properties of small peptides: a molecular dynamics study.
Langmuir. 27, 296-303.
DOI:10.1021/la103800h

AM111.03 Chen, R., Poger, D. and Mark, A.E. (2011)
The Effect of High Pressure on Fully Hydrated DPPC and POPC Bilayers.
J.Phys. Chem. 115, 1038-1044.
DOI:10.1021/jp110002q

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

AM10.05 Groothuizen, F., Poger, D. and Mark, A.E. (2010)
Activating the Prolactin Receptor: Effect of the Ligand on the Conformation of the Extracellular Domain.
J. Chem. Theory Comput. 6, 3274-3283.
DOI:10.1021/ct1003934

AM10.06 Daura, X., Affentrauger, R. and Mark, A.E. (2010)
On the relative merits of equilibrium and non-equilibrium simulations for the estimation of free-energy differences.
ChemPhysChem. 11, 3734-3743.
DOI:10.1002/cphc.201000562

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
media:AM_08_03.pdf

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
media:AM_08_04.pdf

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
media:AM_08_06.pdf

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.
media:AM_07_04.pdf

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.
media:AM_06_04.pdf

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.
media:AM_05_03.pdf

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.
media:AM_05_04.pdf

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.
media:AM_05_05.pdf

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.
media:AM_05_07.pdf

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.
media:AM_05_08.pdf

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.
media:AM_05_09.pdf

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.
media:AM_05_10.pdf

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
media:AM_04_01.pdf

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
media:AM_04_02.pdf

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
media:AM_04_04.pdf

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
media:AM_04_05.pdf

AM04.06 Zangi, R. and Mark, A.E.
Electrofreezing of confined water
J. Chem. Phys. 120 (2004) 7123-7130
media:AM_04_06.pdf

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
media:AM_04_07.pdf

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
media:AM_04_08.pdf

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
media:AM_04_09.pdf

AM04.10 Marrink, S.J. and Mark, A.E.
Molecular view of hexagonal phase formation in phospholipid membranes
Biophys. J. 87 (2004) 3894-3900
media:AM_04_10.pdf

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
media:AM_03_01.pdf

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
media:AM_03_02.pdf

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
media:AM_03_03.pdf

AM03.04 Zangi, R. and Mark, A.E.
Monolayer Ice
Phys. Rev. Letters 91 (2003) art. no. 025502
media:AM_03_04.pdf

AM03.05 Zangi, R. and Mark, A.E.
Bilayer ice and alternate liquid phases of confined water
J. Chem. Phys. 119 (2003) 1694-1700
media:AM_03_05.pdf

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
media:AM_03_06.pdf

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
media:AM_03_07.pdf

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
media:AM_03_08.pdf

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
media:AM_03_09.pdf

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
media:AM_03_10.pdf

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
media:AM_02_01.pdf

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
media:AM_02_02.pdf

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
media:AM_02_03.pdf

AM02.04 Marrink, S.J and Mark, A.E.
Molecular Dynamics Simulations of Mixed Micelles Modeling Human Bile
Biochemistry 41 (2002) 5375-5382
media:AM_02_04.pdf

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
media:AM_02_05.pdf

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
media:AM_02_06.pdf

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
media:AM_02_07.pdf

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
media:AM_02_08.pdf

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
media:AM_02_09.pdf

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)
media:AM_02_10.pdf

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
media:AM_02_11.pdf

AM02.12 van Gunsteren, W.F., Daura, X. and Mark, A.E.
Computation of free energy
Helv. Chim. Acta 85 (2002) 3113-3129
media:AM_02_12.pdf

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
media:AM_02_13.pdf

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
media:AM_01_01.pdf

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
media:AM_01_02.pdf

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
media:AM_01_03.pdf

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
media:AM_01_04.pdf

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
media:AM_01_05.pdf

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
media:AM_01_06.pdf

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
media:AM_01_07.pdf

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
media:AM_01_08.pdf

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
media:AM_01_09.pdf

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
media:AM_00_01.pdf

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
media:AM_00_02.pdf

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
media:AM_00_03.pdf

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
media:AM_00_04.pdf

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
media:AM_00_05.pdf

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

AM94.01 de la Cruz, X., Mark, A.E., Tormo, J., Fita, I. and van Gunsteren, W.F. (1994)
Investigation of the Shape Variations in the Antibody Binding Site by Molecular Dynamics Computer Simulation.
J.Mol. Biol. 226, 1186-1195.

AM94.02 Mark, A.E. and van Gunsteren, W.F. (1994)
Decomposition of the Free Energy System in Terms of Specific Interactions: Implications for Theoretical and Experimental Studies.
J.Mol.Biol.240,167-176.

AM94.03 Beutler, T. C., Mark, A. E., van Schaik, R. C. Gerber, P. R. and van Gunsteren, W. F. (1994)
Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations.
Chem. Phys. Letters. 222, 529-539.

AM94.04 Mark, A. E., van Helden, S. P., Janssen, L. H. M., Smith, P. E. and van Gunsteren, W. F. (1994)
Convergence Properties of Free Energy Calculations: Alpha-Cyclodextrin Complexes as a Case Study.
J. Am. Chem. Soc. 116, 6293-6302.

AM94.05 van Gunsteren, W. F., King, P. M. and Mark, A. E. (1994)
Fundamentals of drug design from a biophysical viewpoint.
Quart. Rev. Biophysics. 27, 435-481.

1993

AM93.01 Shi, Y. Y., Mark, A. E., Wang, C. X., Fuhua, H., Berendsen, H. J. C. and van Gunsteren, W. F. (1993)
Can the stability of protein mutants be predicted by free energy calculations?
Protein Engineering. 3, 289-295.

AM93.02 Smith, P. E., Brunne, R. M., Mark, A. E. and van Gunsteren, W. F. (1993)
The Dielectric Properties of Trypsin Inhibitor and Lysozyme Calculated from Molecular Dynamics Simulations.
J. Phys. Chem. 97, 2009-2014.

AM93.03 Gerber, P. R., Mark, A. E. and van Gunsteren, W. F. (1993)
An approximate but efficient method to calculate free energy trends by computer simulation: Application to dihydrofolate reductase-inhibitor complexes.
J. Comp. Aided. Mol. Des. 7, 305-323.

AM93.04 van Gunsteren, W. F. Beutler, T. C., Fraternali, F., King, P. M, Mark, A. E., and Smith P. E. (1993)
Computation of free energy in practice: choice of approximations and accuracy limiting factors.
In: Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications Vol. 2, van Gunsteren, W. F., Weiner, P. K. and Wilkinson, A. J., eds., Escom Science Publishers, Leiden, The Netherlands.
pp. 315-348.

AM93.05 El Tayar, N., Mark, A. E., Vallat, P., Brunner, R. M, Testa, B. and van Gunsteren, W. F. (1993)
Solvent-Dependent Conformation and Hydrogen Bonding Capacity of Cyclosporin A: Evidence from Partition Coefficients and Molecular Dynamics Simulations.
J. Med. Chem. 36, 3757-3764.

1992

AM92.01 van Gunsteren, W. F. and Mark, A. E. (1992)
On the interpretation of biochemical data by molecular dynamics computer simulation. (review).
Eur. J. Biochem. 204, 947-961.

AM92.02 Vorherr, T., Kessler, O., Mark, A. E. and Carafoli, E. (1992)
Construction and molecular dynamics simulation of calmodulin in the extended and in a bent conformation.
Eur. J. Biochem. 204, 931-937.

AM92.03 van Gunsteren, W. F., Brunne, R. M., Mark, A. E. and van Helden, S. P. (1992)
Computer Simulation of Biomolecules: Comparison with Experimental Data.
In: Molecular Aspects of Biotechnology: Computational Models and Theories Bertran, J. ed., NATO ASI Series C368, Kluwer Academic Publishers, Dordrecht, pp.105-122.

AM92.04 van Gunsteren, W. F. and Mark, A. E. (1992)
Prediction of the activity and stability effects of site-directed mutagenisis on a protein core.
J. Mol. Biol. 227, 389-395.

AM92.05 Mark, A. E. and van Gunsteren, W. F. (1992)
Simulation of the Thermal Denaturation of Hen Egg White Lysozyme: Trapping the Molten Globule State.
Biochemistry. 31, 7745-7748.

1991

AM91.01 Mark, A. E., van Gunsteren, W. F. and Berendsen, H. J. C. (1991)
Calculation of Relative Free Energy via Indirect Pathways.
J. Chem. Phys. 94, 3808-3816.

AM91.02 Mark, A. E., Berendsen, H. J. C, Heiner, A. P and van Gunsteren, W.F. (1991)
Calculation of Relative Free Energy by Molecular Dynamics.
Proc. 7th Intl. Symp. on “Metabolism and Enzymology of Nucleic Acids Including Gene and Protein Engineering”. Balan, J. ed., Inst. of Mol. Biol. Slovak Academy of Sciences, Bratislava, 25-38.

AM91.03 Mark, A. E., Berendsen, H. J. C. and van Gunsteren, W. F. (1991)
Conformational flexibility of aqueous monomeric and dimeric insulin: A molecular dynamics study.
Biochemistry. 30, 10866-10872.

1990

AM90.01 Mark, A. E., Nichol, L. W. and Jeffrey, P. D. (1990)
The reversible cross-linking of receptors by ligands: Theory for the prediction of binding responses.
Biochem. Int. 22, 685-697.

AM90.02 Mark, A. E. and Jeffrey, P. D. (1990)
The self-association of zinc-free bovine insulin: Four model patterns and their significance.
Biol. Chem. Hoppe. Seyler. 371,1165-1174.

1988

AM.88.01 Mark, A. E., Jeffrey, P. D. and Nichol, L. W. (1988)
The binding of an indefinitely associating ligand to an acceptor: Consideration of a monovalent ligand species binding to a multivalent acceptor.
J. Theor. Biol. 131, 137-149.

1987

AM.87.01 Mark, A. E., Nichol, L. W. and Jeffrey, P. D. (1987)
The self-association of zinc-free bovine insulin: A single model based on interactions in the crystal that describes the association pattern in solution at pH 2, 7 and 10.
Biophys. Chem. 27, 103-117.

1986

AM.86.01 Mark, A. E. (1986)
Binding responses associated with self-interacting ligands.
Thesis, ANU.

1984

AM.84.01 Stone, S. R., Mark, A. E. and Morrison, J. F. (1984)
Interaction of analogues of nicotinamide adenine-dinucleotide phosphate with dihydrofolate-reductase from Escherichia-coli.
Biochemistry. 23, 4340-4346.