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2011 Journal Article Using theory to reconcile experiment : The structural and thermodynamic basis of ligand recognition by phenylethanolamine N -methyltransferase (PNMT)Nair, Pramod C., Malde, Alpeshkumar K. and Mark, Alan E. (2011). Using theory to reconcile experiment : The structural and thermodynamic basis of ligand recognition by phenylethanolamine N -methyltransferase (PNMT). Journal of Chemical Theory and Computation, 7 (5), 1458-1468. doi: 10.1021/ct1007229 |
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2011 Journal Article The effect of membrane curvature on the conformation of antimicrobial peptides: Implications for binding and the mechanism of actionChen, Rong and Mark, Alan E. (2011). The effect of membrane curvature on the conformation of antimicrobial peptides: Implications for binding and the mechanism of action. European Biophysics Journal, 40 (4), 545-553. doi: 10.1007/s00249-011-0677-4 |
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2011 Journal Article Effect of high pressure on fully hydrated DPPC and POPC bilayersChen, Rong, Poger, David and Mark, Alan (2011). Effect of high pressure on fully hydrated DPPC and POPC bilayers. The Journal of Physical Chemistry B, 115 (5), 1038-1044. doi: 10.1021/jp110002q |
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2011 Journal Article Effect of poly(ethylene glycol) (PEG) spacers on the conformational properties of small peptides: A molecular dynamics studyXue, Ying, O'Mara, Megan L., Surawski, Peter P. T., Trau, Matt and Mark, Alan E. (2011). Effect of poly(ethylene glycol) (PEG) spacers on the conformational properties of small peptides: A molecular dynamics study. Langmuir, 27 (1), 296-303. doi: 10.1021/la103800h |
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2011 Journal Article Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexesMalde, AK and Mark, AE (2011). Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexes. Journal of Computer-Aided Molecular Design, 25 (1), 1-12. doi: 10.1007/s10822-010-9397-6 |
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2010 Journal Article On the relative merits of equilibrium and non-equilibrium simulations for the estimation of free-energy differencesDaura, Xavier, Affentranger, Roman and Mark, Alan E. (2010). On the relative merits of equilibrium and non-equilibrium simulations for the estimation of free-energy differences. ChemPhysChem, 11 (17), 3734-3743. doi: 10.1002/cphc.201000562 |
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2010 Journal Article Activating the prolactin receptor: Effect of the ligand on the conformation of the extracellular domainGroothuizen, Flora S., Poger, David and Mark, Alan E. (2010). Activating the prolactin receptor: Effect of the ligand on the conformation of the extracellular domain. Journal of Chemical Theory and Computation, 6 (10), 3274-3283. doi: 10.1021/ct1003934 |
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2010 Journal Article Basic ingredients of free energy calculations: A reviewChrist, Clara D., Mark, Alan E. and van Gunsteren, Wilfred F. (2010). Basic ingredients of free energy calculations: A review. Journal of Computational Chemistry, 31 (8), 1569-1582. doi: 10.1002/jcc.21450 |
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2010 Journal Article A new force field for simulating phosphatidylcholine bilayersPoger, David, van Gunsteren, Wilfred F. and Mark, Alan E. (2010). A new force field for simulating phosphatidylcholine bilayers. Journal of Computational Chemistry, 31 (6), 1117-1125. doi: 10.1002/jcc.21396 |
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2010 Journal Article Turning the growth hormone receptor on: Evidence that hormone binding induces subunit rotationPoger, David and Mark, Alan E. (2010). Turning the growth hormone receptor on: Evidence that hormone binding induces subunit rotation. Proteins: Structure, Function & Bioinformatics, 78 (5), 1163-1174. doi: 10.1002/prot.22636 |
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2010 Journal Article On the validation of molecular dynamics simulations of saturated and cis-monounsaturated phosphatidylcholine lipid bilayers: A comparison with experimentPoger, David and Mark, Alan E. (2010). On the validation of molecular dynamics simulations of saturated and cis-monounsaturated phosphatidylcholine lipid bilayers: A comparison with experiment. Journal of Chemical Theory and Computation, 6 (1), 325-336. doi: 10.1021/ct900487a |
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2009 Journal Article Penrose-Hameroff orchestrated objective-reduction proposal for human consciousness is not biologically feasibleMcKemmish, Laura K., Reimers, Jeffrey R., McKenzie, Ross H., Mark, Alan E. and Hush, Noel S. (2009). Penrose-Hameroff orchestrated objective-reduction proposal for human consciousness is not biologically feasible. Physical Review E, 80 (2) 021912, 1-5. doi: 10.1103/PhysRevE.80.021912 |
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2009 Journal Article 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 (vol 113, pg 1728, 2009)Periole, Xavier, Rampioni, Aldo, Vendruscolo, Michele and Mark, Alan E. (2009). 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 (vol 113, pg 1728, 2009). Journal of Physical Chemistry B, 113 (30), 10548-10548. doi: 10.1021/jp905822d |
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2009 Journal Article Alternative mechanisms for the interaction of the cell-penetrating peptides penetratin and the TAT peptide with lipid bilayersYesylevskyy, Semen, Marrink, Siewert-Jan and Mark, Alan E. (2009). Alternative mechanisms for the interaction of the cell-penetrating peptides penetratin and the TAT peptide with lipid bilayers. Biophysical Journal, 97 (1), 40-49. doi: 10.1016/j.bpj.2009.03.059 |
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2009 Journal Article Inclusion of ionization states of ligands in affinity calculationsDonnini, Serena, Villa, Alessandra, Groenhof, Gerrit, Mark, Alan E., Wierenga, Rik K. and Juffer, Andre H. (2009). Inclusion of ionization states of ligands in affinity calculations. Proteins: Structure, Function and Bioinformatics, 76 (1), 138-150. doi: 10.1002/prot.22326 |
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2009 Journal Article Probing the free energy landscape of the FBP28WW domain using multiple techniquesPeriole, Xavier, Allen, Lucy R., Tamiola, Kamil, Mark, Alan E. and Paci, Emanuele (2009). Probing the free energy landscape of the FBP28WW domain using multiple techniques. Journal of Computational Chemistry, 30 (7), 1059-1068. doi: 10.1002/jcc.21128 |
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2009 Journal Article Disturb or stabilize? A molecular dynamics study of the effects of resorcinolic lipids on phospholipid bilayersSiwko, Magdalena E., de Vries, Alex H., Mark, Alan E., Kozubek, Arkadiusz and Marrink, Siewert J. (2009). Disturb or stabilize? A molecular dynamics study of the effects of resorcinolic lipids on phospholipid bilayers. Biophysical Journal, 96 (8), 3140-3153. doi: 10.1016/j.bpj.2009.01.040 |
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2009 Journal Article Weak, strong, and coherent regimes of Frohlich condensation and their applications to terahertz medicine and quantum consciousnessReimers, Jeffrey R., McKemmish, Laura K., McKenzie, Ross H., Mark, Alan E. and Hush, Noel S. (2009). Weak, strong, and coherent regimes of Frohlich condensation and their applications to terahertz medicine and quantum consciousness. Proceedings of the National Academy of Sciences of USA, 106 (11), 4219-4224. doi: 10.1073/pnas.0806273106 |
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2009 Journal Article Binding and enantiomeric selectivity of threonyl-tRNA synthetaseMalde, Alpeshkumar K. and Mark, Alan E. (2009). Binding and enantiomeric selectivity of threonyl-tRNA synthetase. Journal of the American Chemical Society, 131 (11), 3848-3849. doi: 10.1021/ja9002124 |
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2009 Journal Article Factors that affect the degree of twist in beta-sheet structures: A molecular dynamics simulation study of a cross-beta filament of the GNNQQNY peptidePeriole, Xavier, Rampioni, Aldo, Vendruscolo, Michele and Mark, Alan E. (2009). 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 Part B, 113 (6), 1728-1737. doi: 10.1021/jp8078259 |
