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2009 Journal Article Calcium binding to the purple membrane: A molecular dynamics studyWassenaar, Tsjerk A., Daura, Xavier, Padros, Esteve and Mark, Alan E. (2009). Calcium binding to the purple membrane: A molecular dynamics study. Proteins Structure Function Bioinformatics, 74 (3), 669-681. doi: 10.1002/prot.22182 |
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2008 Journal Article Toroidal pores formed by antimicrobial peptides show significant disorderSengupta, Durba, Leontidaou, Hari, Mark, Alan E. and Marrink, Siewert-Jan (2008). Toroidal pores formed by antimicrobial peptides show significant disorder. Biochimica et Biophysica Acta: Biomembranes, 2008 (1778), 2308-2317. doi: 10.1016/j.bbamem.2008.06.007 |
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2008 Journal Article The Cys3-Cys4 loop of the hydrophobin EAS is not required for rodlet formation and surface activityKwan, Ann H., Macindoe, Ingrid, Vukasin, Paul V., Morris, Vanessa K., Kass, Itamar, Gupte, Rima, Mark, Alan E., Templeton, Matthew D., Mackay, Joel P. and Sunde, Margaret (2008). The Cys3-Cys4 loop of the hydrophobin EAS is not required for rodlet formation and surface activity. Journal of Molecular Biology, 382 (3), 708-720. doi: 10.1016/j.jmb.2008.07.034 |
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2008 Journal Article Application of mean field boundary potentials in simulations of lipid vesiclesRisselada, H. Jelger, Mark, Alan E. and Marrink, Siewert J. (2008). Application of mean field boundary potentials in simulations of lipid vesicles. The Journal of Physical Chemistry B, 112 (25), 7438-7447. doi: 10.1021/jp0758519 |
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2008 Journal Article The structure of a two-disulfide intermediate assists in elucidating the oxidative folding pathway of a cyclic cystine knot proteinCemazar, M., Joshi, A., Daly, N. L., Mark, A. E. and Craik, D. J. (2008). The structure of a two-disulfide intermediate assists in elucidating the oxidative folding pathway of a cyclic cystine knot protein. Structure, 16 (6), 842-851. doi: 10.1016/j.str.2008.02.023 |
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2008 Journal Article Refining homology models by combining replica-exchange molecular dynamics and statistical potentialsZhu, 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 Bioinformatics, 72 (72), 1171-1188. doi: 10.1002/prot.22005 |
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2008 Journal Article Electrophoretic mobility does not always reflect the charge on an oil dropletKnecht, V., Risselda, 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 (2), 477-486. doi: 10.1016/j.jcis.2007.10.035 |
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2008 Journal Article Molecular simulation as an aid to experimentalistsvan Gunsteren, W.F., Dolenc, J. and Mark, A.E. (2008). Molecular simulation as an aid to experimentalists. Current Opinion In Structural Biology, 2008 (18), 149-153. doi: 10.1016/j.sbi.2007.12.007 |
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2008 Journal Article The conformation of the extracellular binding domain of Death Receptor 5 in the presence and absence of the activating ligand TRAIL: A molecular dynamics studyWassenaar, Tsjerk A., Quax, Wim J. and Mark, Alan 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 (2), 333-343. doi: 10.1002/prot.21541 |
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2008 Journal Article Histidine protonation and the activation of viral fusion proteinsMueller, D., Kampmann, T., Yennamalli, R., Young, P.R., Kobe, B. and Mark, A. E. (2008). Histidine protonation and the activation of viral fusion proteins. Biochemical Society Transactions, 36 (1), 43-45. doi: 10.1042/BST0360043 |
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2007 Journal Article Applications of free energy calculations to chemistry and biologyChipot, Christophe, Mark, Alan E., Pande, Vijay S. and Simonson, Thomas (2007). Applications of free energy calculations to chemistry and biology. Springer Series in Chemical Physics, 86, 463-501. doi: 10.1007/978-3-540-38448-9_13 |
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2007 Journal Article Ion transport across transmembrane poresLeontiadou, H, Mark, AE and Marrink, SJ (2007). Ion transport across transmembrane pores. Biophysical Journal, 92 (12), 4209-4215. doi: 10.1529/biophysj.106.101295 |
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2007 Journal Article How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field?Villa, A, Fan, H, Wassenaar, T and Mark, AE (2007). How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field?. Journal of Physical Chemistry B, 111 (21), 6015-6025. doi: 10.1021/jp068580v |
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2007 Journal Article On the characterization of host-guest complexes: Surface tension, calorimetry, and molecular dynamics of cyclodextrins with a non-ionic surfactantPineiro, Ángel, Banquy, Xavier, Perez-Casas, Silvia, Tovar, Edgar, Garcia, Abel, Villa, Alessandra, Amigo, Alfredo, Mark, Alan E. and Costas, Miguel (2007). On the characterization of host-guest complexes: Surface tension, calorimetry, and molecular dynamics of cyclodextrins with a non-ionic surfactant. Journal of Physical Chemistry B, 111 (17), 4383-4392. doi: 10.1021/jp0688815 |
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2007 Journal Article Molecular dynamics simulations from putative transition states of alpha-spectrin SH3 domainPeriole, X, Vendruscolo, M and Mark, AE (2007). Molecular dynamics simulations from putative transition states of alpha-spectrin SH3 domain. Proteins-structure Function And Bioinformatics, 69 (3), 536-550. doi: 10.1002/prot.21491 |
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2007 Journal Article Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solventPeriole, X and Mark, AE (2007). Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent. Journal of Chemical Physics, 126 (1) 014903, 014903-1-014903-11. doi: 10.1063/1.2404954 |
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2007 Journal Article Does isoprene protect plant membranes from thermal shock? A molecular dynamics studySiwko, M. E., Marrink, S. J., de Vries, A. H., Kozubek, A., Uiterkamp, A. J. M. S. and Mark, A. E. (2007). Does isoprene protect plant membranes from thermal shock? A molecular dynamics study. Biochimica Et Biophysica Acta-biomembranes, 1768 (2), 198-206. doi: 10.1016/j.bbamem.2006.09.023 |
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2006 Journal Article New Algorithms for Macromolecular Simulation - PrefaceLeimkuhler, Benedict, Chipot, Christophe, Elber, Ron, Laaksonen, Aatto, Mark, Alan, Schlick, Tamar, Schütte, Christof and Skeel, Robert (2006). New Algorithms for Macromolecular Simulation - Preface. Lecture Notes in Computational Science and Engineering, 49, v-vii. |
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2006 Journal Article Mimicking the action of GroEL in molecular dynamics simulations: Application to the refinement of protein structuresFan, Hao and Mark, Alan E. (2006). Mimicking the action of GroEL in molecular dynamics simulations: Application to the refinement of protein structures. Protein Science, 15 (3), 441-448. doi: 10.1110/ps.051721006 |
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2006 Journal Article The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditionsWassenaar, T. A. and Mark, A. E. (2006). The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions. Journal of Computational Chemistry, 27 (3), 316-325. doi: 10.1002/jcc.20341 |
