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Oostenbrink, C., Villa, A., Mark, A. E. and Van Gunsteren, W. F. (2004) 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, 25 13: 1656-1676. doi:10.1002/jcc.20090 355   1054 Cited 1099 times in Scopus1099 0
Schafer, Heiko, Mark, Alan E. and van Gunsteren, Wilfred F. (2000) Absolute entropies from molecular dynamics simulation trajectories. Journal of Chemical Physics, 113 18: 7809-7817. doi:10.1063/1.1309534 265 1 124 Cited 129 times in Scopus129 0
Feenstra, K. A., Peter, C., Scheek, R. M., van Gunsteren, W. F. and Mark, A. E. (2002) A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities) in small peptides. Journal of Biomolecular Nmr, 23 3: 181-194. doi:10.1023/A:1019854626147 233   28 Cited 28 times in Scopus28 0
Groothuizen, 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 116   2 Cited 2 times in Scopus2 0
Poger, David and Mark, Alan E. (2014) Activation of the epidermal growth factor receptor: a series of twists and turns. Biochemistry, 53 16: 2710-2721. doi:10.1021/bi401632z 75   0 Cited 0 times in Scopus0 0
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. Organic & Biomolecular Chemistry, 3 7: 1189-1194. doi:10.1039/b418167k 83   20 Cited 20 times in Scopus20 0
Saez, Natalie J., Mobli, Mehdi, Bieri, Michael, Chassagnon, Irene R., Malde, Alpeshkumar K., Gamsjaeger, Roland, Mark, Alan E., Gooley, Paul R., Rash. Lachlan D. and King, Glenn F. (2011) A dynamic pharmacophore drives the interaction between psalmotoxin-1 and the putative drug target acid-sensing ion channel 1a. Molecular Pharmacology, 80 5: 796-808. doi:10.1124/mol.111.072207 141   21 Cited 23 times in Scopus23 0
Yesylevskyy, 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.2009.03.059 100   69 Cited 72 times in Scopus72 0
Pineiro, 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. Biophysical Journal, 89 6: 3701-3713. doi:10.1529/biophysj.104.055590 107   18 Cited 18 times in Scopus18 0
Kovalskyy, D., Dubyna, V., 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 Bioinformatics, 58 2: 450-458. doi:10.1002/prot.20304 123   11 Cited 10 times in Scopus10 0
Malde, Alpeshkumar K., Zuo, Le, Breeze, Matthew, Stroet, Martin, Poger, David, Nair, Pramod C., Oostenbrink, Chris and Mark, Alan E. (2011) An automated force field topology builder (ATB) and repository: Version 1.0. Journal of Chemical Theory and Computation, 7 12: 4026-4037. doi:10.1021/ct200196m 151   95 Cited 100 times in Scopus100 2
Fioroni, Marco, Burger, Klaus, Mark, Alan E. and Roccatano, Danilo (2000) A new 2,2,2-triflouroethanol model for molecular dynamics simulations. The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces and Biophysical, 104 51: 12347-12354. doi:10.1021/jp002115v 95 20 72 Cited 72 times in Scopus72 0
Poger, 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 139   63 Cited 79 times in Scopus79 0
Leontiadou, H., Mark, A. E. and Marrink, S. J. (2006) Antimicrobial peptides in action. Journal of The American Chemical Society, 128 37: 12156-12161. doi:10.1021/ja062927q 150   204 Cited 211 times in Scopus211 1
Risselada, 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 82   33 Cited 34 times in Scopus34 0
Chipot, C., Mark, A. E., Pande, V. S. and Simonson, T. (2007). Applications of Free Energy Calculations to Chemistry and Biology.. In Christophe Chipot and Andrew Pohorille (Ed.), Free Energy Calculations Theory and Applications in Chemistry and Biology (pp. 463-492) Berlin ; New York: Springer. 162  
Kampmann, T., Muller, D. A., Robinson, J., Mark, A., Young, P. R. and Kobe, B. (2005). A structural model for low pH mediated viral fusion: The role of histidine protonation. In: 3rd Australian Virology Group Meeting. 3rd Australian Virology Group Meeting, Phillip Island, (Abstract). 9-12 Dec, 2005. 136  
Christ, 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 123   103 Cited 114 times in Scopus114 0
Zangi, R. and Mark, A. E. (2003) Bilayer ice and alternate liquid phases of confined water. Journal of Chemical Physics, 119 3: 1694-1700. doi:10.1063/1.1580101 124   63 Cited 64 times in Scopus64 0
Malde, 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 87   7 Cited 7 times in Scopus7 0
Wassenaar, 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 94   3 Cited 3 times in Scopus3 0
Villa, A. and Mark, A. E. (2002) Calculation of the free energy of solvation for neutral analogs of amino acid side chains. Journal of Computational Chemistry, 23 5: 548-553. doi:10.1002/jcc.10052 129   89 Cited 93 times in Scopus93 0
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 4: 738-746. doi:10.1002/cbic.200400244 117   23 Cited 24 times in Scopus24 0
Malde, 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/s10822-010-9397-6 103   16 Cited 15 times in Scopus15 8
Canzar, Stefan, El-Kebir, Mohammed, Pool, René, Elbassioni, Khaled, Malde, Alpeshkumar K., Mark, Alan E., Geerke, Daan P., Stougie, Leen and Klau, Gunnar W. (2013) Charge group partitioning in biomolecular simulation. Journal of Computational Biology, 20 3: 188-198. doi:10.1089/cmb.2012.0239 94   6 Cited 6 times in Scopus6 2
Canzar, Stefan, El-Kebir, Mohammed, Pool, Rene, Elbassioni, Khaled, Malde, Alpesh K., Mark, Alan E., Geerke, Daan P., Stougie, Leen and Klau, Gunnar W. (2012). Charge group partitioning in biomolecular simulation. In: Benny Chor, Proceedings: 16th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2012. 16th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2012, Barcelona, Spain, (29-43). 21 - 24 April 2012. doi:10.1007/978-3-642-29627-7_3 114   Cited 0 times in Scopus0 1
Marrink, S. J., de Vries, A. H. and Mark, A. E. (2004) Coarse grained model for semiquantitative lipid simulations. Journal of Physical Chemistry B, 108 2: 750-760. doi:10.1021/jp036508g 225   835 Cited 838 times in Scopus838 3
Fan, Hao, Mark, Alan E., Zhu, Jiang and Honig, Barry (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. doi:10.1073/pnas.0408857102 123 1 55 Cited 59 times in Scopus59 0
Riniker, Sereina, Christ, Clara D., Hansen, Niels, Mark, Alan E., Nair, Pramod C. and van Gunsteren, Wilfred F. (2011) Comparison of enveloping distribution sampling and thermodynamic integration to calculate binding free energies of phenylethanolamine N-methyltransferase inhibitors. Journal of Chemical Physics, 135 2: 024105.1-024105.13. doi:10.1063/1.3604534 106   18 Cited 19 times in Scopus19 0
van Gunsteren, W. F., Daura, X. and Mark, A. E. (2002) Computation of free energy. Helvetica Chimica Acta, 85 10: 3113-3129. 106   61
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. Journal of Physical Chemistry B, 110 3: 1423-1428. doi:10.1021/jp052722o 118   22 Cited 23 times in Scopus23 0
Periole, 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: 014903-1-014903-11. doi:10.1063/1.2404954 232   49 Cited 56 times in Scopus56 0
Schmid, Nathan, Eichenberger, Andreas P., Choutko, Alexandra, Riniker, Sereina, Winger, Moritz, Mark, Alan E. and van Gunsteren, Wilfred F. (2011) Definition and testing of the GROMOS force-field versions 54A7 and 54B7. European Biophysics Journal, 40 7: 843-856. doi:10.1007/s00249-011-0700-9 104   148 Cited 149 times in Scopus149 1
Yennamalli, RM, Kobe, B, Mark, AE, Young, PR and Subbarao, N (2009). Dengue viral envelope protein and histidine protonation. In: Indian Journal of Virology. XVIII National Conference of Indian Virological Society, Post Graduate Institute of Medical Education and Research, Chandigarh, India., (29-29). 11–13 December 2008. 157   0
Xue, Ying, He, Lizhong, Middelberg, Anton P. J., Mark, Alan E. and Poger, David (2014) Determining the structure of interfacial peptide films: comparing neutron reflectometry and molecular dynamics simulations. Langmuir, 30 33: 10080-10089. doi:10.1021/la501715h 54   0 Cited 0 times in Scopus0 2
Siwko, 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 94   9 Cited 10 times in Scopus10 0
Siwko, 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.2006.09.023 121   41 Cited 44 times in Scopus44 0
Jena, Nihar R., Mark, Alan E. and Mishra, Phool C. (2014) Does tautomerization of FapyG influence its mutagenicity?. ChemPhysChem, 15 9: 1779-1784. doi:10.1002/cphc.201400045 60   0 Cited 0 times in Scopus0 1
van den Berg, P. A. W., Feenstra, K. A., Mark, A. E., Berendsen, H. J. C. and Visser, A. J. W. G. (2002) Dynamic conformations of flavin adenine dinucleotide: Simulated molecular dynamics of the flavin cofactor related to the time-resolved fluorescence characteristics. Journal of Physical Chemistry B, 106 34: 8858-8869. doi:10.1021/jp020356s 196   69 Cited 70 times in Scopus70 0
Chen, 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 95 2 13 Cited 12 times in Scopus12 0
Poger, David, Caron, Bertrand and Mark, Alan E. (2014) Effect of methyl-branched fatty acids on the structure of lipid bilayers. Journal of Physical Chemistry B, 118 48: 13838-13848. doi:10.1021/jp503910r 67   0 Cited 0 times in Scopus0 0
Xue, 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 114   10 Cited 11 times in Scopus11 0
Marrink, S. J. and Mark, A. E. (2001) Effect of undulations on surface tension in simulated bilayers. Journal of Physical Chemistry B, 105 26: 6122-6127. doi:10.1021/jp0103474 104   185 Cited 185 times in Scopus185 0
Zangi, R. and Mark, A. E. (2004) Electrofreezing of confined water. Journal of Chemical Physics, 120 15: 7123-7130. doi:10.1063/1.1687315 139   47 Cited 50 times in Scopus50 0
Knecht, 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.2007.10.035 318   23 Cited 25 times in Scopus25 0
Schafer, H., Daura, X., Mark, A. E. and van Gunsteren, W. F. (2001) Entropy calculations on a reversibly folding peptide: Changes in solute free energy cannot explain folding behavior. Proteins-structure Function And Genetics, 43 1: 45-56. doi:10.1002/1097-0134(20010401)43:1<45::AID-PROT1016>3.0.CO;2-N 110   79 Cited 78 times in Scopus78 0
Schafer, H., Smith, L. J., Mark, A. E. and van Gunsteren, W. F. (2002) Entropy calculations on the molten globule state of a protein: Side-chain entropies of alpha-lactalbumin. Proteins-structure Function And Genetics, 46 2: 215-224. doi:10.1002/prot.1166 179   42 Cited 47 times in Scopus47 0
Jia, Z. G., O'Mara, M. L., Zuegg, J., Matthew Cooper and Mark, Alan (2013) Erratum: The effect of environment on the recognition and binding of vancomycin to native and resistant forms of lipid II (Biophysical Journal (2011) 101 (2684-2692)). Biophysical Journal, 104 2: 516-516. doi:10.1016/j.bpj.2012.12.031 91   0 Cited 0 times in Scopus0 0
de Groot, B. L., Daura, X., Mark, A. E. and Grubmuller, H. (2001) Essential dynamics of reversible peptide folding: Memory-free conformational dynamics governed by internal hydrogen bonds. Journal of Molecular Biology, 309 1: 299-313. doi:10.1006/jmbi.2001.4655 135   77 Cited 84 times in Scopus84 0
Schäfer, Heiko, Van Gunsteren, Wilfred F. and Mark, Alan E. (1999) Estimating relative free energies from a single ensemble: Hydration free energies. Journal of Computational Chemistry, 20 15: 1604-1617. doi:10.1002/(SICI)1096-987X(19991130)20:15<1604::AID-JCC2>3.0.CO;2-A 70 1 50 Cited 49 times in Scopus49 0

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