PublicationsMark: Difference between revisions
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== '''In press''' == | == '''In press''' == | ||
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== '''2003''' == | == '''2003''' == | ||
'''AM03.01''' Colombo, G., Marrink, S.J. and Mark, A.E.<br/>Simulation of Mscl Gating in a Bilayer under Stress<br/>Biophys. J. 84 (2003) 2331-2337<br/> | '''AM03.01''' Colombo, G., Marrink, S.J. and Mark, A.E.<br/>Simulation of Mscl Gating in a Bilayer under Stress<br/>Biophys. J. 84 (2003) 2331-2337<br/>[[media:AM_03_01.pdf]] | ||
'''AM03.02''' Fioroni, M, Burger, K, Mark, A.E. and Roccatano, D.<br/>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<br/>J. Phys. Chem. B 107 (2003) 4855-4861<br/>[[media:AM_03_02.pdf]] | |||
'''AM03. | '''AM03.03''' Tieleman, D.P., Leontiadou, H., Mark, A.E. and Marrink, S.J.<br/>Simulation of the Pore Formation in Lipid Bilayers by Mechanical Stress and Electric Fields<br/>J. Am. Chem. Soc. 125 (2003) 6382-6383<br/>[[media:AM_03_03.pdf]] | ||
'''AM03.04''' Zangi, R. and Mark, A.E.<br/>Monolayer Ice<br/>Phys. Rev. Letters 91 (2003) art. no. 025502<br/>[[media:AM_03_04.pdf]] | |||
'''AM03. | '''AM03.05''' Zangi, R. and Mark, A.E.<br/>Bilayer ice and alternate liquid phases of confined water<br/>J. Chem. Phys. 119 (2003) 1694-1700<br/>[[media:AM_03_05.pdf]] | ||
'''AM03.06''' Fan, H. and Mark, A.E.<br/>Relative Stability of Protein Structures Determined by X-ray Crystallography or NMR Spectroscopy: A Molecular Dynamics Simulation Study<br/>Proteins 53 (2003) 111-120<br/>[[media:AM_03_06.pdf]] | |||
'''AM03. | '''AM03.07''' Talhout, R., Villa, A., Mark, A.E. and Engberts, J.B.F.N.<br/>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<br/>J. Am. Chem. Soc. 125 (2003) 10570-10579<br/>[[media:AM_03_07.pdf]] | ||
'''AM03.08''' Marrink, S.J. and Mark, A.E.<br/>The Mechanism of Vesicle Fusion as Revealed by Molecular Dynamics Simulations<br/>J. Am. Chem. Soc. 125 (2003) 11144-11145<br/>[[media:AM_03_08.pdf]] | |||
'''AM03. | '''AM03.09''' Marrink, S.J. and Mark, A.E.<br/>Molecular Dynamics Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles<br/>J. Am. Chem. Soc. 125 (2003) 15233-15242<br/>[[media:AM_03_09.pdf]] | ||
'''AM03.10''' Villa, A., Zangi, R., Pieffert, G. and Mark, A.E.<br/>Sampling and convergence in free energy calculations of protein-ligand interactions: The binding of triphenoxypyridine derivatives to Factor Xa and Trypsin<br/>J. Comp. Aided Mol. Des. 17 (2003) 673-686<br/>[[media:AM_03_10.pdf]] | |||
== '''2002''' == | == '''2002''' == |
Revision as of 00:31, 22 July 2008
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