PublicationsMark

We are currently in the process of updating our electronic records. Please do not hesitate to email Sophie Turner at md.secretary@uq.edu.au if you have any questions. Any information about electronic copies of articles currently missing from the list would also be appreciated.

In press

• Wassenaar, T., Daura, X., Padrós, E. and Mark, A. E. (2008)

Calcium binding to the Purple Membrane: A Molecular Dynamics study. PROTEINS (in press)

• Zhu, J., Fan, H., Xavier, P., Honig, B., Mark, A. E. (2008)

Refining Homology Models by Combining Replica-Exchange Molecular Dynamics and Statistical Potentials PROTEINS (Accepted)

• Cemazar, M., Joshi, A., Daly, N., Mark, A. E. and Craik, D. (2008)

The Structure of a two-disulfide intermediate assists in elucidating the oxidative folding pathway of a cyclic cystine knot protein. Structure (in press)

• Risselada, H.J., Mark, A.E. and Marrink, S.J. (2008)

The application of MFFA boundary potentials in MD simulations of lipid Vesicales. J. of Phys. Chem. B (in press)

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, 111, 6015-6025.
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

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

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

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

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

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

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

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

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

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

2000

Coming soon

1999

Coming soon

1998

Coming soon

1997

Coming soon

1996

Coming soon

1995

Coming soon

1993

Coming soon

1992

Coming soon

1991

Coming soon

1990

Coming soon

1988

Coming soon

1987

Coming soon

1986

Coming soon

1984

Coming soon