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Alan Mark

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

Research Profile (preview)

Activities & Behaviors

Computer Simulation

Concepts & Ideas

Occupations

Thermodynamics

Chemicals & Drugs

Physiology

Protein Folding

Anatomy

Lipid Bilayers

Phenomena

Hydrogen Bonding

Genes & Molecular Sequences

Amino Acid Sequence

Procedures

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Network (preview)

Co-Publications
Name
25
van Gunsteren, Wilfred
21
Marrink, Siewert
7
Fan, Hao
7
Daura, Xavier
7
Villa, Alessandra
5
Zangi, Ronen
5
Berendsen, Herman
5
Periole, Xavier
5
Leontiadou, Hari
4
de Vries, André
4
Groenhof, Gerrit
4
Wassenaar, Tsjerk
3
Colombo, Giorgio
3
Roccatano, Danilo
3
Knecht, Volker

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Publications

TOP 3
Yesylevskyy Semen; Marrink Siewert-Jan; Mark Alan E
Alternative mechanisms for the interaction of the cell-penetrating peptides penetratin and the TAT peptide with lipid bilayers.
Periole Xavier; Allen Lucy R; Tamiola Kamil; Mark Alan E; Paci Emanuele
Probing the free energy landscape of the FBP28WW domain using multiple techniques.
Siwko Magdalena E; de Vries Alex H; Mark Alan E; Kozubek Arkadiusz; Marrink Siewert J
Disturb or stabilize? A molecular dynamics study of the effects of resorcinolic lipids on phospholipid bilayers.

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All Publications

2009: Yesylevskyy Semen; Marrink Siewert-Jan; Mark Alan E
Alternative mechanisms for the interaction of the cell-penetrating peptides penetratin and the TAT peptide with lipid bilayers.
Biophysical journal 2009;97(1):40-9.
2009: Periole Xavier; Allen Lucy R; Tamiola Kamil; Mark Alan E; Paci Emanuele
Probing the free energy landscape of the FBP28WW domain using multiple techniques.
Journal of computational chemistry 2009;30(7):1059-68.
2009: Siwko Magdalena E; de Vries Alex H; Mark Alan E; Kozubek Arkadiusz; Marrink Siewert J
Disturb or stabilize? A molecular dynamics study of the effects of resorcinolic lipids on phospholipid bilayers.
Biophysical journal 2009;96(8):3140-53.
2009: Periole Xavier; Rampioni Aldo; Vendruscolo Michele; Mark Alan E
Factors that affect the degree of twist in beta-sheet structures: a molecular dynamics simulation study of a cross-beta filament of the GNNQQNY peptide.
The journal of physical chemistry. B 2009;113(6):1728-37.
2009: Wassenaar Tsjerk A; Daura Xavier; Padrós Esteve; Mark Alan E
Calcium binding to the purple membrane: A molecular dynamics study.
Proteins 2009;74(3):669-81.
2008: Sengupta Durba; Leontiadou Hari; Mark Alan E; Marrink Siewert-Jan
Toroidal pores formed by antimicrobial peptides show significant disorder.
Biochimica et biophysica acta 2008;1778(10):2308-17.
2008: Zhu Jiang; Fan Hao; Periole Xavier; Honig Barry; Mark Alan E
Refining homology models by combining replica-exchange molecular dynamics and statistical potentials.
Proteins 2008;72(4):1171-88.
2008: Risselada H Jelger; Mark Alan E; Marrink Siewert J
Application of mean field boundary potentials in simulations of lipid vesicles.
The journal of physical chemistry. B 2008;112(25):7438-47.
2008: van Gunsteren Wilfred F; Dolenc Jozica; Mark Alan E
Molecular simulation as an aid to experimentalists.
Current opinion in structural biology 2008;18(2):149-53.
2008: Mueller Daniela S; Kampmann Thorsten; Yennamalli Ragothaman; Young Paul R; Kobe Bostjan; Mark Alan E
Histidine protonation and the activation of viral fusion proteins.
Biochemical Society transactions 2008;36(Pt 1):43-5.
2008: Knecht V; Risselada H J; Mark A E; Marrink S J
Electrophoretic mobility does not always reflect the charge on an oil droplet.
Journal of colloid and interface science 2008;318(2):477-86.
2008: Wassenaar Tsjerk A; Quax Wim J; Mark Alan E
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 2008;70(2):333-43.
2007: Periole Xavier; Vendruscolo Michele; Mark Alan E
Molecular dynamics simulations from putative transition states of alpha-spectrin SH3 domain.
Proteins 2007;69(3):536-50.
2007: Leontiadou Hari; Mark Alan E; Marrink Siewert-Jan
Ion transport across transmembrane pores.
Biophysical journal 2007;92(12):4209-15.
2007: Villa Alessandra; Fan Hao; Wassenaar Tsjerk; Mark Alan E
How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field?
The journal of physical chemistry. B 2007;111(21):6015-25.
2007: Siwko Magdalena E; Marrink Siewert J; de Vries Alex H; Kozubek Arkadiusz; Schoot Uiterkamp Anton J M; Mark Alan E
Does isoprene protect plant membranes from thermal shock? A molecular dynamics study.
Biochimica et biophysica acta 2007;1768(2):198-206.
2007: Periole Xavier; Mark Alan E
Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent.
The Journal of chemical physics 2007;126(1):014903.
2006: Leontiadou Hari; Mark Alan E; Marrink Siewert J
Antimicrobial peptides in action.
Journal of the American Chemical Society 2006;128(37):12156-61.
2006: Fan Hao; Wang Xiaoqin; Zhu Jiang; Robillard George T; Mark Alan E
Molecular dynamics simulations of the hydrophobin SC3 at a hydrophobic/hydrophilic interface.
Proteins 2006;64(4):863-73.
2006: Fan Hao; Mark Alan E
Mimicking the action of GroEL in molecular dynamics simulations: application to the refinement of protein structures.
Protein science : a publication of the Protein Society 2006;15(3):441-8.
2006: Knecht Volker; Mark Alan E; Marrink Siewert-Jan
Phase behavior of a phospholipid/fatty acid/water mixture studied in atomic detail.
Journal of the American Chemical Society 2006;128(6):2030-4.
2006: Wassenaar Tsjerk A; Mark Alan E
The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions.
Journal of computational chemistry 2006;27(3):316-25.
2006: Villa Alessandra; Mark Alan E; Saracino Gloria A A; Cosentino Ugo; Pitea Demetrio; Moro Giorgio; Salmona Mario
Conformational polymorphism of the PrP106-126 peptide in different environments: a molecular dynamics study.
The journal of physical chemistry. B 2006;110(3):1423-8.
2005: Van Der Spoel David; Lindahl Erik; Hess Berk; Groenhof Gerrit; Mark Alan E; Berendsen Herman J C
GROMACS: fast, flexible, and free.
Journal of computational chemistry 2005;26(16):1701-18.
2005: Piñeiro Angel; Villa Alessandra; Vagt Toni; Koksch Beate; Mark Alan E
A molecular dynamics study of the formation, stability, and oligomerization state of two designed coiled coils: possibilities and limitations.
Biophysical journal 2005;89(6):3701-13.
2005: Marrink Siewert J; Risselada Jelger; Mark Alan E
Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model.
Chemistry and physics of lipids 2005;135(2):223-44.
2005: Fan Hao; Mark Alan E; Zhu Jiang; Honig Barry
Comparative study of generalized Born models: protein dynamics.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(19):6760-4.
2005: de Vries Alex H; Yefimov Serge; Mark Alan E; Marrink Siewert J
Molecular structure of the lecithin ripple phase.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(15):5392-6.
2005: Pagel Kevin; Seeger Karsten; Seiwert Bettina; Villa Alessandra; Mark Alan E; Berger Stefan; Koksch Beate
Advanced approaches for the characterization of a de novo designed antiparallel coiled coil peptide.
Organic & biomolecular chemistry 2005;3(7):1189-94.
2005: van den Bosch Marieke; Swart Marcel; Snijders Jaap G; Berendsen Herman J C; Mark Alan E; Oostenbrink Chris; van Gunsteren Wilfred F; Canters Gerard W
Calculation of the redox potential of the protein azurin and some mutants.
Chembiochem : a European journal of chemical biology 2005;6(4):738-46.
2005: Soto Patricia; Cladera Josep; Mark Alan E; Daura Xavier
Stability of SIV gp32 fusion-peptide single-layer protofibrils as monitored by molecular-dynamics simulations.
Angewandte Chemie (International ed. in English) 2005;44(7):1065-7.
2005: Knecht Volker; Müller Michiel; Bonn Mischa; Marrink Siewert-Jan; Mark Alan E
Simulation studies of pore and domain formation in a phospholipid monolayer.
The Journal of chemical physics 2005;122(2):024704.
2004: Marrink Siewert-Jan; Mark Alan E
Molecular view of hexagonal phase formation in phospholipid membranes.
Biophysical journal 2004;87(6):3894-900.
2004: Oostenbrink Chris; Villa Alessandra; Mark Alan E; van Gunsteren Wilfred F
A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6.
Journal of computational chemistry 2004;25(13):1656-76.
2004: Zangi Ronen; Mark Alan E
Electrofreezing of confined water.
The Journal of chemical physics 2004;120(15):7123-30.
2004: de Vries Alex H; Mark Alan E; Marrink Siewert J
Molecular dynamics simulation of the spontaneous formation of a small DPPC vesicle in water in atomistic detail.
Journal of the American Chemical Society 2004;126(14):4488-9.
2004: Groenhof Gerrit; Bouxin-Cademartory Mathieu; Hess Berk; De Visser Sam P; Berendsen Herman J C; Olivucci Massimo; Mark Alan E; Robb Michael A
Photoactivation of the photoactive yellow protein: why photon absorption triggers a trans-to-cis Isomerization of the chromophore in the protein.
Journal of the American Chemical Society 2004;126(13):4228-33.
2004: Leontiadou Hari; Mark Alan E; Marrink Siewert J
Molecular dynamics simulations of hydrophilic pores in lipid bilayers.
Biophysical journal 2004;86(4):2156-64.
2004: Fan Hao; Mark Alan E
Mimicking the action of folding chaperones in molecular dynamics simulations: Application to the refinement of homology-based protein structures.
Protein science : a publication of the Protein Society 2004;13(4):992-9.
2004: Fan Hao; Mark Alan E
Refinement of homology-based protein structures by molecular dynamics simulation techniques.
Protein science : a publication of the Protein Society 2004;13(1):211-20.
2003: Marrink Siewert J; Mark Alan E
Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles.
Journal of the American Chemical Society 2003;125(49):15233-42.
2003: Villa Alessandra; Zangi Ronen; Pieffet Gilles; Mark Alan E
Sampling and convergence in free energy calculations of protein-ligand interactions: the binding of triphenoxypyridine derivatives to factor Xa and trypsin.
Journal of computer-aided molecular design 2003;17(10):673-86.
2003: Fan Hao; Mark Alan E
Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: a molecular dynamics simulation study.
Proteins 2003;53(1):111-20.
2003: Marrink Siewert J; Mark Alan E
The mechanism of vesicle fusion as revealed by molecular dynamics simulations.
Journal of the American Chemical Society 2003;125(37):11144-5.
2003: Talhout Reinskje; Villa Alessandra; Mark Alan E; Engberts Jan 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.
Journal of the American Chemical Society 2003;125(35):10570-9.
2003: Zangi Ronen; Mark Alan E
Monolayer ice.
Physical review letters 2003;91(2):025502.
2003: Tieleman D Peter; Leontiadou Hari; Mark Alan E; Marrink Siewert-Jan
Simulation of pore formation in lipid bilayers by mechanical stress and electric fields.
Journal of the American Chemical Society 2003;125(21):6382-3.
2003: Colombo Giorgio; Marrink Siewert Jan; Mark Alan E
Simulation of MscL gating in a bilayer under stress.
Biophysical journal 2003;84(4):2331-7.
2002: Roccatano Danilo; Colombo Giorgio; Fioroni Marco; Mark Alan E
Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary-structure formation in peptides: a molecular dynamics study.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(19):12179-84.
2002: Groenhof Gerrit; Lensink Marc F; Berendsen Herman J C; Mark Alan E
Signal transduction in the photoactive yellow protein. II. Proton transfer initiates conformational changes.
Proteins 2002;48(2):212-9.
2002: Groenhof Gerrit; Lensink Marc F; Berendsen Herman J C; Snijders Jaap G; Mark Alan E
Signal transduction in the photoactive yellow protein. I. Photon absorption and the isomerization of the chromophore.
Proteins 2002;48(2):202-11.
2002: Feenstra K Anton; Peter Christine; Scheek Ruud M; van Gunsteren Wilfred F; Mark Alan E
A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities) in small peptides.
Journal of biomolecular NMR 2002;23(3):181-94.
2002: Zangi Ronen; de Vocht Marcel L; Robillard George T; Mark Alan E
Molecular dynamics study of the folding of hydrophobin SC3 at a hydrophilic/hydrophobic interface.
Biophysical journal 2002;83(1):112-24.
2002: Marrink S J; Mark A E
Molecular dynamics simulations of mixed micelles modeling human bile.
Biochemistry 2002;41(17):5375-82.
2002: Villa Alessandra; Mark Alan E
Calculation of the free energy of solvation for neutral analogs of amino acid side chains.
Journal of computational chemistry 2002;23(5):548-53.
2002: Colombo Giorgio; Roccatano Danilo; Mark Alan E
Folding and stability of the three-stranded beta-sheet peptide Betanova: insights from molecular dynamics simulations.
Proteins 2002;46(4):380-92.
2002: Schäfer Heiko; Smith Lorna J; Mark Alan E; van Gunsteren Wilfred F
Entropy calculations on the molten globule state of a protein: side-chain entropies of alpha-lactalbumin.
Proteins 2002;46(2):215-24.
2001: Marrink S J; Lindahl E; Edholm O; Mark A E
Simulation of the spontaneous aggregation of phospholipids into bilayers.
Journal of the American Chemical Society 2001;123(35):8638-9.
2001: Roccatano D; Mark A E; Hayward S
Investigation of the mechanism of domain closure in citrate synthase by molecular dynamics simulation.
Journal of molecular biology 2001;310(5):1039-53.
2001: Zangi R; Kovacs H; van Gunsteren W F; Johansson J; Mark A E
Free energy barrier estimation of unfolding the alpha-helical surfactant-associated polypeptide C.
Proteins 2001;43(4):395-402.
2001: de Groot B L; Daura X; Mark A E; Grubmüller H
Essential dynamics of reversible peptide folding: memory-free conformational dynamics governed by internal hydrogen bonds.
Journal of molecular biology 2001;309(1):299-313.
2001: Schäfer H; Daura X; Mark A E; van Gunsteren W F
Entropy calculations on a reversibly folding peptide: changes in solute free energy cannot explain folding behavior.
Proteins 2001;43(1):45-56.
2000: Walser R; Mark A E; 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.
Biophysical journal 2000;78(6):2752-60.
1999: Daura X; Antes I; van Gunsteren W F; Thiel W; Mark A E
The effect of motional averaging on the calculation of NMR-derived structural properties.
Proteins 1999;36(4):542-55.
1999: Daura X; van Gunsteren W F; Mark A E
Folding-unfolding thermodynamics of a beta-heptapeptide from equilibrium simulations.
Proteins 1999;34(3):269-80.
1998: Daura X; Jaun B; Seebach D; van Gunsteren W F; Mark A E
Reversible peptide folding in solution by molecular dynamics simulation.
Journal of molecular biology 1998;280(5):925-32.
1997: Kovacs H; Mark A E; van Gunsteren W F
Solvent structure at a hydrophobic protein surface.
Proteins 1997;27(3):395-404.
1995: Hünenberger P H; Mark A E; van Gunsteren W F
Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations.
Journal of molecular biology 1995;252(4):492-503.
1995: Smith L J; Mark A E; Dobson C M; van Gunsteren W F
Comparison of MD simulations and NMR experiments for hen lysozyme. Analysis of local fluctuations, cooperative motions, and global changes.
Biochemistry 1995;34(34):10918-31.
1995: Van Gunsteren W F; Hünenberger P H; Kovacs H; Mark A E; Schiffer C A
Investigation of protein unfolding and stability by computer simulation.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 1995;348(1323):49-59.
1995: Kovacs H; Mark A E; Johansson J; 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.
Journal of molecular biology 1995;247(4):808-22.
1995: Hünenberger P H; Mark A E; van Gunsteren W F
Computational approaches to study protein unfolding: hen egg white lysozyme as a case study.
Proteins 1995;21(3):196-213.
1995: Mark A E; Xu Y; Liu H; van Gunsteren W F
Rapid non-empirical approaches for estimating relative binding free energies.
Acta biochimica Polonica 1995;42(4):525-35.
1994: van Gunsteren W F; King P M; Mark A E
Fundamentals of drug design from a biophysical viewpoint.
Quarterly reviews of biophysics 1994;27(4):435-81.
1994: Mark A E; van Gunsteren W F
Decomposition of the free energy of a system in terms of specific interactions. Implications for theoretical and experimental studies.
Journal of molecular biology 1994;240(2):167-76.
1994: de la Cruz X; Mark A E; Tormo J; Fita I; van Gunsteren W F
Investigation of shape variations in the antibody binding site by molecular dynamics computer simulation.
Journal of molecular biology 1994;236(4):1186-95.
1993: el Tayar N; Mark A E; Vallat P; Brunne R M; Testa B; van Gunsteren W F
Solvent-dependent conformation and hydrogen-bonding capacity of cyclosporin A: evidence from partition coefficients and molecular dynamics simulations.
Journal of medicinal chemistry 1993;36(24):3757-64.
1993: Gerber P R; Mark A E; van Gunsteren W F
An approximate but efficient method to calculate free energy trends by computer simulation: application to dihydrofolate reductase-inhibitor complexes.
Journal of computer-aided molecular design 1993;7(3):305-23.
1993: Shi Y Y; Mark A E; Wang C X; Huang F; Berendsen H J; van Gunsteren W F
Can the stability of protein mutants be predicted by free energy calculations?
Protein engineering 1993;6(3):289-95.
1992: Mark A E; van Gunsteren W F
Simulation of the thermal denaturation of hen egg white lysozyme: trapping the molten globule state.
Biochemistry 1992;31(34):7745-8.
1992: van Gunsteren W F; Mark A E
Prediction of the activity and stability effects of site-directed mutagenesis on a protein core.
Journal of molecular biology 1992;227(2):389-95.
1992: van Gunsteren W F; Mark A E
On the interpretation of biochemical data by molecular dynamics computer simulation.
European journal of biochemistry / FEBS 1992;204(3):947-61.
1991: Mark A E; Berendsen H J; van Gunsteren W F
Conformational flexibility of aqueous monomeric and dimeric insulin: a molecular dynamics study.
Biochemistry 1991;30(45):10866-72.

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